The 27-year-old - who scored her first number one last year with Burn - took the trophy four years after collecting her first Brit.
The ceremony is the biggest night in the UK music calendar with dozens of stars and thousands of fans gathered at the O2 Arena in London.
Goulding collected her prize from Prince and his group 3RDEYEGIRL who are in the UK to perform a series of intimate surprise shows at well-known venues.
The award-winner told guests: "Thank you so much - I genuinely am in shock - I'm not very good at this at all. This means so much to me - I can't even tell you."
She beat acts such as Jessie J and Laura Marling to the prize.
Arctic Monkeys opened the show with a performance of their track R U Mine? with flaming letters spelling out the name of their fifth album AM.
As ceremony host James Corden took the stage he jokingly turned up with a blazing sleeve which was put out by security staff. And as Prince arrived to read out the nominees he whipped out a phone and took a "selfie" alongside him.
Katy Perry was also among the performers, playing her single Dark Horse with a fluorescent Egyptian themed stage set, flanked by costumed dancers.
Corden even posted the image of himself and Prince on Twitter during the show, captioning it: "Selfie x"
US star Bruno Mars was named best international male act, an award he had previously collected in 2012.
After accepting the prize from Kylie Minogue - who wore a knee-length black rubber dress - and Pharrell Williams, Mars told the audience: "I want to thank the fans. We love coming out here, we love performing for you all."
Four-piece act Bastille collected the prize for best British breakthrough, beating acts such as Disclosure and London Grammar.
Singer Dan Smith - who like the rest of his band were shocked by the win - said: "This time last year I don't think anyone in this room including us even thought we would be here."
Corden - who was hosting the awards for a fourth successive year and is stepping down as regular host - brought whoops from the crowd when he sat with One Direction in a gap between awards, asking them if they had any advice for troubled singer Justin Bieber who is on bail after being arrested for drink and driving offences.
The group's Louis Tomlinson said: "Keep strong and keep doing what you're doing."
Corden spluttered: "Don't keep doing what you're doing Justin - that's the worst advice ever."
Arctic Monkeys were named best British group - the third time they have collected the trophy having won it in 2007 and 2008 - beating acts such as One Direction.
The band - who won a new set of fans on the back of fifth album AM - have previously collected awards in fancy dress, with former appearances in hunting gear and dressed as Village People. However this time they opted for smart suits.
Frontman Alex Turner joked: "That's 15 quid we put on One Direction to win down the drain."
He acknowledged there were many people they should thank, but added: "They need to hear their names read out as much as you need to hear a list of people you don't know."
They collected the award from Lily Allen, sporting a yellow pony tail, who experienced a less than slick moment during the glitzy awards when she was unsure what to do when it came to reading out the shortlist, asking: "Do I just go straight into it?"
One Direction suffered a toilet mishap when Harry Styles was still visiting the loo while the rest of his group was collecting the band's global success award.
When they took the stage as a four-piece, the group's Liam Payne asked: "Has anyone seen the curly haired lad? I don't know where you are Harry."
Styles then came hurtling up a runway to the stage and told the audience: "I'm really sorry I was having a wee. Toilets are ages away. What did we win?
"A massive thank you to all our fans," he added.
Corden then poked up at the star's lothario reputation, adding: Having a wee? He couldn't even wait 'til the end of the show."
Here is the full list of winners:
:: British Male Solo Artist:
:: British Female Solo Artist:
:: British Group:
:: British Breakthrough Act:
:: British Single
Rudimental featuring Ella Eyre - Waiting All Night
:: British Album Of The Year:
Arctic Monkeys - AM
:: Global success:
:: Best Video:
One Direction - Best Song Ever
:: International Male Solo Artist:
:: International Female Solo Artist:
:: International Group:
:: Critics' Choice:
:: British Producer Of The Year:
Flood & Alan Moulder