Jurors at the phone-hacking trial will still decide whether Brooks, 45, is guilty of four further offences - one count of conspiring to hack phones, two of perverting the course of justice, and one of conspiring to commit misconduct in a public office.
Judge Mr Justice Saunders, sitting at the Old Bailey, instructed the jury to formally acquit Brooks. The charge relates to an allegation that she sanctioned a payment of £4,000 to a public official for a picture of Prince William dressed as a bikini-clad Bond girl at a Sandhurst party.
The image was not published, though it led to an exclusive in The Sun in September 2006 - the tabloid Brooks edited before taking the helm at its sister paper - with the headline "Willy in a Bikini" together with a mocked-up picture of the prince wearing a green swimsuit and Hawaiian-style flowers.
The judge said a verdict of "not guilty" had to be returned for Brooks on that count.
He said: "I have decided that there is no case for Ms Brooks to answer on count four. That is the charge relating to a picture of Prince William in a bikini.
"Whether or not there is a case to answer is for me to decide."
Brooks stood and smiled as the jury foreman recorded a not guilty verdict.
Jonathan Laidlaw QC made an opening statement at the start of Brooks's defence case today, saying jurors might have found the trial hard to follow so far.
He told the court that "on occasions absolutely critical information was overlooked or left out" by the prosecution.
Mr Laidlaw said: "If there is a sense of confusion about the evidence and what it is said to relate to, that would be entirely understandable."
He told the jury that at the end of the trial, he would "have a lot more to say" about Brooks's treatment by the prosecution and the police.
Mr Laidlaw told the jury it was not for Brooks to give evidence to "make out her innocence", but that the prosecution must bear the burden of reaching a high standard of proof.
He said: "That may not be something that has emerged clearly or at all at this point."
Mr Laidlaw told the jury: "Although these allegations arose in the court of Mrs Brooks's employment, she is not being tried, is she, because she was the editor of a tabloid newspaper?
"Views, as we all understand, differ about the tabloid press, and the worth or otherwise of the tabloid press within the broad spectrum of the media.
"Neither is she on trial for having worked for Rupert Murdoch's company or for having worked her way up, literally from the bottom, through that organisation.
"She is not being tried for News International's strategy, for its policies, its influences, or its corporate views.
"Politics next. Neither is Mrs Brooks on trial for any political views she may hold, neither is she to be judged for the support that the newspapers she edited gave to one particular political party at one time or another."
The barrister told the jurors that the list was not exhaustive, but he wanted to show them how important it was that they remained focused and not distracted.
He added: "There is, isn't there, an awful lot which is going on in the background to this case and in its shadow?
"There are agendas as you can all see, being pursued elsewhere, so please just be careful and keep an open mind and stay focused upon what matters."
Mr Laidlaw told the jury it is important for them to see the ex-tabloid editor "as she is" and "begin the process of working out whether there is any truth in any of the allegations made against her".
Mr Laidlaw told the jury: "It is for you to see Mrs Brooks as she is - not as she has been described or spoken of elsewhere."
He said the key questions for them were firstly did she "know about and endorse a practice of phone hacking at the News of the World during her editorship from May 2000 to January 2003"; did she know that a public official was the source for a story at the Sun, and did she instruct her husband Charlie and personal assistant Cheryl Carter to cover up evidence of phone hacking or paying public official?
Brooks was then sworn into the witness box.
She confirmed she was born in Warrington, Cheshire, in 1968 and was an only child.
Sitting in the witness box wearing a white cardigan over a blue dress with her red hair pinned back, Brooks told the jury: "My grandmother who I said lived with us, she was a writer. She wrote a lot of poetry, and she wrote a poetry column for a local newspaper. The idea probably stemmed from her."
She said she had "swept the floors and made the tea" at the local newspaper. Brooks said she got her first full-time job in journalism in 1988, when she was around 20.
Brooks told the jury that her father was a gardener and her mother a personal assistant.
Her parents split when she was aged 21 and her mother went to London where Brooks was then living. Her father is now dead.
She told her mother at the age of eight that she wanted to be a writer, Brooks said.
Brooks recalled getting work experience at a local newspaper, the Warrington Guardian, at the age of 14.
As Brooks described her early days in journalism, her husband and co-defendant Charlie Brooks sat with his left hand resting against the side of his head, smiling.
Mrs Brooks said The Post newspaper, where she got her first job, proved to be a "short-lived" publication. But while there, she started to do research for senior journalists when they were going out on a story, such as checking cuttings, and said she was "bit by bit allowed to write a paragraph".
Asked by Mr Laidlaw if she was enthusiastic, she said: "Quite enthusiastic, yes, very enthusiastic."
The court heard that she next went to work for the News of the World's Sunday magazine, starting in April 1989. News of the World staff who worked with her at the Post but returned to the NotW after the paper's closure "put in a good word" for her.
She got her job on the NotW magazine as a features researcher.
At the time, the features department was known as the "pink parlour", she said, because there were more women working there.
Despite the NotW editor being a woman at the time, the newsroom was still male-dominated, she said.
While working, Brooks took a course at the London College of Printing but she added: "Learning on the job was more informative."
Brooks told the court that she was made aware very early on of the importance of contacts for journalists, both at college and as she worked at the News of the World's magazine, when she heard colleagues talk about "their contacts and their sources".
She said that although she was mainly working on features, the importance was further emphasised later as she met "journalists who seemed to have contacts everywhere and sources everywhere".
Asked if she was keen to develop relationships with those people she had interviewed, she said: "I think with the 'establish contacts' in the back of my head from all around me, I think if you did interview someone and you got on well and they liked the piece that you had written then you stayed in touch and maybe they would come back a bit later...".
She said that was unlikely to happen if they had not liked the piece that was written, but said if they did like it "normally you could make them a contact or they would become a contact".
The court heard that when her then-editor moved to be deputy editor at the News of the World newspaper, Brooks asked if she could move with her to work on the newspaper's features desk.
In September 1989 Brooks was promoted to feature writer for the magazine supplement.
Describing her work for the magazine, she said: "What I ended up doing was interviewing people. The magazine, it was a mixture of celebrity interviews, or we did a lot of human interest stories, or a combination.
"If you could get a celebrity in a human interest story that was pretty good."
In 1992 Brooks moved over to the features department for the main paper and became deputy features editor in 1994.
Features was responsible for "the furniture" of the newspaper including motoring, travel, gardening and agony aunt. She described it as "back of the book" content.
But news and features also competed for front page stories too, she said.