The pictures of the prince frolicking in the nude with an unnamed woman in Las Vegas made headlines around the world but until now no papers in the UK had used them following a request from St James's Palace, made via the press watchdog, to respect Harry's privacy.
The Rupert Murdoch-owned tabloid said it was carrying the pictures in today's edition so the millions of people who get their news in print or have no internet access could "take a full part in that national conversation".
One of the two naked images of the royal is splashed across the front page of the newspaper, just a day after the publication got a member of staff to pose for its front page in a mock up.
It carries the headline: "Heir it is!" with an editorial explaining the reasons behind their decision to print it.
It reads: "The photos have potential implications for the Prince's image representing Britain around the world.
"There are questions over his security during the Las Vegas holiday. Questions as to whether his position in the Army might be affected. Further, we believe Harry has compromised his own privacy."
Adding it was "vital" that the paper ran the pictures, the editorial continued: "The Prince Harry pictures are a crucial test of Britain's free Press.
"It is absurd that in the internet age newspapers like The Sun could be stopped from publishing stories and pictures already seen by millions on the free-for-all that is the web."
St James's Palace said it was down to the editors of Britain's newspapers to decide whether they printed the controversial pictures.
A palace spokesman added: "We have made our views on Prince Harry's privacy known. Newspapers regulate themselves, so the publication of the photographs is ultimately a decision for editors to make."
Sun managing editor David Dinsmore said the paper had "thought long and hard" about whether to use the pictures and said it was an issue of freedom of the press rather than because it was moralising about Harry's actions.
He said: "The Sun is a responsible paper and it works closely with the royal family. We take heed of their wishes.
"We're also big fans of Prince Harry, he does a huge amount of work for this country and for the military and for the image of both of those institutions.
"We are not against him letting his hair down once in a while. For us this is about the freedom of the press.
"This is about our readers getting involved in discussion with the man who's third in line to the throne, it's as simple as that."
The newspaper's decision to publish the images provoked mixed reaction among those both and in and outside the media industry.
Former deputy prime minister Lord Prescott said The Sun had shown "absolute utter contempt" for the law and for the Lord Justice Leveson inquiry into media ethics.
"It is not about privacy. It is about money, money, money. And they know that by exclusively printing the pictures, assuming they are the only (British) paper which does, they will get everybody buying the paper to see this."
Meanwhile, Former Sun editor Kelvin MacKenzie welcomed the move. "If Prince Harry with no clothes on in a Las Vegas hotel room surrounded by one naked woman and a load of other people he has just met in drinking-stripping game is not a story then it is hard to know what is," he told BBC's Newsnight.
"He must realise that with his rather important role as a prince of our country and is number three (in line) to the throne that he has to carry various responsibilities.
"People should stop worrying about privacy and start worrying about what free speech will mean to this country if the Levesons and the Camerons of this country have their way."
Press standards campaign group Hacked Off also hit out at The Sun's actions.
Its director, Brian Cathcart, said: "This is the country's biggest-selling newspaper breaking the industry's own code despite clear warnings. It is flagrant proof that our national newspapers are incapable of regulating their own affairs.
"The Sun's argument that this is about freedom of the press is nonsense.
"This is about the Sun's right to trample over the industry's own feeble rules when it likes, and also to invade people's privacy whenever it chooses."
Media lawyer Mark Lewis, who has represented a number of phone hacking victims, said The Sun's decision to print the pictures was motivated purely by money.
He told BBC Radio 5Live: "This isn't about press freedom, this is all about there is money to be made from publishing it (the picture).
"I'm sure The Sun will sell out today by people who have not seen it on the internet and who are curious - It's ultimately all about profit."
Mr Lewis said he did not believe the decision by other UK publications to not publish the images was related to the Leveson inquiry.
He added: "Other newspapers are showing good taste and decided to respect the wishes of a family that said please don't publish these pictures and The Sun have seen there are pots of money to be made by publishing them.
"This is yesterday's news, why didn't The Sun print them yesterday? Is it saying it didn't have press freedom yesterday to run it and now it has press freedom?"
Meanwhile, further details of the night the pictures were taken have emerged.
A witness who claimed to be at the party inside the prince's Las Vegas hotel suite said there were around 25 people in the room when he took off his clothes.
They also revealed details about how the royal's security team failed to take any mobile phones from party-goers.
The witness told The Sun: "No one asked for our phones or anything about us when we arrived at the party. It was obvious people were taking pictures."
Publicist Max Clifford said today it was "ludicrous" that the pictures had been so widely available on the internet before The Sun chose to publish them.
Speaking on Daybreak, he said: "We're the only country in the world where you can't read about it in the papers. It's a bit of a ludicrous situation.
"Now we'll have to see what the Palace will do. You can only assume that the Palace are going to sue The Sun. It will be interesting to see how it develops."
He said there was a "huge public interest" in the story, but added: "It is an invasion of privacy in my view, clearly."
Mr Clifford said Harry's charity work and military service was a credit to the Royal Family, telling the ITV1 programme: "I think he's done us proud. I think we should have respected his privacy.
"I understand why The Sun has done it - they're going to sell a lot more papers. But does that make it right?"
Louise Mensch, a Tory MP on the Culture, Media and Sport Committee, backed the Sun's decision to publish the pictures, claiming there was a "clear and demonstrable" public interest in the story.
She told BBC Radio 4's Today programme: "I'm chilled to hear the Press Complaints Commission (PCC) tried to tread on this story and they should not have done it.
"The PCC after the Leveson Inquiry really ought not to be in the business of collectively telling newspaper editors they can't run a story and they shouldn't use their best judgment.
"That is the real sin in this story and The Sun was right to publish."
Mrs Mensch, who is standing down as an MP, said she believed Parliament would fight any recommendation of a regulated press system if one was recommended by Lord Justice Leveson.
The Leveson Inquiry report into the press is expected to be published later this year.
Jonathan Collett, director of communications at the PCC, told the same programme: "What the PCC did in this case was follow normal procedures.
"We've developed a sophisticated pre-publication procedure which has been praised at the Leveson Inquiry, whereby if people at the heart of a news story who have concerns there might be a potential breach of the code, they can communicate through the PCC and we pass on their concerns to editors, so editors can then use their own judgment as to whether they may be potentially breaking the code.
"This is not the PCC putting pressure or steering people, this is the PCC passing on concerns of people at the heart of the story."
Mr Collett said if a formal complaint was made after publication, then the PCC would look at the case in detail, including relevant case law - which Mr Collett said had to be taken in its full context.
Until now, the public has been able to read about the prince's antics but to see the images has had to access the US-based celebrity gossip website TMZ that broke the story, or scores of other internet pages across the globe.
It was widely believed that editors had shied away from publishing the photos in respect of past rulings on privacy along with the ongoing Leveson Inquiry.
Ireland's Evening Herald was one publication that bucked the trend, splashing a picture of the prince on Wednesday's front page. Its deputy editor Ian Mallon said it had carried the image out out a duty to the readers.Scottish-based media magazine The Drum also carried an image online.
Despite The Sun's stance on the issue, the majority of UK publications are still refraining from printing the images.
Its main rival The Mirror said it took the decision not to publish the pictures as doing so would be "in clear breach" of the Press Complaints Commission's Editors' Code of Practice, regarding intrusion of privacy. A poll by the red-top found 63% of people believed UK newspapers should not be banned from printing the pictures.
The Independent also followed in the footsteps of The Mirror, saying there was an issue of privacy relating to the images.
TMZ said the photos were taken last Friday after the prince and his entourage met some women in a hotel bar and invited them up to the royal's suite.
The group played a stripping game and someone in the party is thought to have captured the images of the naked prince on a camera phone.
In the first photograph, which is published on the Sun's front page, the royal is shown wearing just a necklace and a wristband with his hands around his genitals as a seemingly topless woman stands close behind him.
The nude prince is shown in another picture shielding himself behind an unknown woman who is also naked, with his bare bottom facing the camera.
But there is no suggestion that anything other than horseplay is going on between the royal and the unnamed woman.
Although the incident is embarrassing for Harry, who is due to embark on the next phase of his military career, there are unlikely to be any serious consequences for him beyond accusations of a lack of judgment.
If any action is taken against the 27-year-old, an Army officer and Apache helicopter pilot, it would be down to his commanding officer to make the decision.