Welsh singer Duffy's single Mercy has been named song of the year at Mojo magazine's awards in central London.
The soul singer lost out in the best breakthrough act category to The Last Shadow Puppets - the side project of Arctic Monkeys singer Alex Turner.
And she was beaten to best album by Nick Cave and the Bad Seeds.
Other acts honoured at the reader-voted Mojo Honours List bash at The Brewery included Led Zeppelin, Paul Weller, the Sex Pistols and Genesis.
As she collected her award, Duffy said she had "never won anything" in her life.
Led Zeppelin's John Paul Jones (l) and Jimmy Page picked up the band's prize
The 24-year-old dedicated her win to her father, who is retiring after running a club in her home town, Nefyn, for 35 years.
"He tells me he's only got four bingos left," she said. "So this is for him tonight and thanks everyone for your support."
Mojo's editor-in-chief Phil Alexander told the audience Mercy won because it was "a timeless song".
"It could really have come from any period in time over the last 50 years," he said.
Led Zeppelin, who reunited at London's O2 arena at the end of 2007, won best live act.
Guitarist Jimmy Page accepted the trophy with bassist John Paul Jones, and hinted that he would like to get back on stage with the band.
Asked whether there would be more live shows, Page replied: "Let's hope they can vote for us for live awards in the future.
They influenced every aspect of popular culture from fashion to the media, film and literature and on to the music industry itself
Mojo editor Phil Alexander on the Sex Pistols
"The only thing with Led Zeppelin is you've got to have the four members - and Robert Plant, the singer, is out doing another [tour] and has been since the early part of this year."
The place of drummer John Bonham, who died in 1980, was taken by his son Jason for the O2 reunion.
Veteran heavy metal band Motorhead, described by Mr Alexander as "a unique force", were honoured with Mojo's hero award.
And the Sex Pistols, who played to more than 50,000 people at the Isle of Wight Festival on Saturday, won the icon award.
"As punk's standard-bearers, the Sex Pistols truly redefined modern music in the space of one solitary album," Mr Alexander said.
"They influenced every aspect of popular culture from fashion to the media, film and literature and on to the music industry itself."
Speaking after the ceremony, lead singer John Lydon, aka Johnny Rotten, bemoaned the smoking ban, which came into force last July.
"You can't smoke in the building, you can't smoke in your own car," he said.
"They used to be worried about what you smoked and now it's just smoking, period."
Maverick award
And Neil Diamond, 67, who last month topped the UK album chart for the first time with new release Home Before Dark, won the classic songwriter award.
Ska band The Specials, meanwhile, followed in the footsteps of acts including The Doors and Elton John as they were welcomed into the Mojo Hall of Fame.
"Everyone wishes that the Specials were still around now," Mr Alexander said.
"Not only was their music terrific but they stood for something in terms of what they had to say."
Rock band Genesis - who have sold about 150 million albums worldwide - won a lifetime achievement award.
Lead singer Phil Collins revealed the secret of his career was down to "a lot of luck".
He added: "I'm getting hungry to write."
Other winners included Paul Weller, for his outstanding contribution to music, and former Creedence Clearwater Revival frontman John Fogerty, who won the inspiration award for his contribution to rock music.
The Fall frontman Mark E Smith won the maverick award, while the soundtrack to Oscar-nominated film Juno won compilation of the year.
Bookmark with:
What are these?