Co-written with producer Paul Epworth, 'Skyfall' is the first ever 007 theme to win an Academy Award.
"Thank you so much, this is amazing," Adele said, before starting her thanks and bursting into tears.
"I'd just like to thank Barbara Broccoli and Michael Wilson at Eon, Sony Pictures, MGM and Paul Epworth... And my man, I love you, baby!"
Thanking the Broccolis and Sony staff, Epworth continued: "I can't really believe I'm up here to receive this.
"I've got to thank my wife Danielle and my daughter Vivienne... [also] Joe and Matt who spent hours working on this [song]... and most of all I'd like to thank Adele for being the best person I've ever worked with, she's absolutely amazing."
Adele concluded: "You're all amazing, thank you very much!"
Past Bond themes to be nominated, but fail to win, have included Paul McCartney and Wings's Live and Let Die' in 1973, 'Nobody Does It Better' from The Spy Who Loved Me in 1977 and Sheena Easton's 'For Your Eyes Only' in 1982.
'Skyfall' was a favourite to win this year's Oscar, having already been recognised at the Golden Globes and last week's Brit Awards, which Adele failed to attend as she was in the US rehearsing for her performance of the track at tonight's ceremony.
Watch Adele perform 'Skyfall' live at the 2013 Oscars below:
Oscars 2013 red carpet arrivals - photo gallery: