The 23rd movie in the series became the first to win the outstanding British film award, beating formidable competition from musical blockbuster Les Miserables in something of a surprise victory.
It was also the first Bafta the franchise has won since From Russia With Love picked up the best cinematography prize in 1963, despite 42 nominations.
The movie, the third starring Daniel Craig as the suave spy, is already the highest-grossing film of all time at the UK box office.
Director Sam Mendes paid tribute to the actor’s “bravery and brilliance” and “the great”author Ian Fleming, who created 007, as he accepted the gong,
Speaking backstage later, Mendes said he would love to make another Bond film.
“I’ve had a great time, it’s been a huge learning curve and we would want to make a better movie next time around, and if we thought we do that they might let me have another go again,” he said.
Skyfall also picked up the prize for best original music.
The award for best actor went to Daniel Day-Lewis for his title role in Steven Spielberg’s political biopic Lincoln.
The star poked fun at his reputation for immersing himself in his characters as he accepted his trophy.
“On the chance I might one day have to speak on an evening such as this I’ve stayed in character as myself for the last 55 years,” he said.
French actress Emmanuelle Riva was named best actress for her performance in Amour in a surprise victory for the 85-year-old, who did not attend the ceremony.
Ben Affleck completed a hat-trick of wins by picking up the best director prize for his Iran hostage drama Argo to go with his recent Golden Globe and Directors’ Guild of America awards.
Such successes are normally a near guarantee of Oscars glory, but Affleck failed to even land a nomination for the coveted Academy Award for best director.
Affleck, who rose to fame as an actor, said: “I want to say this is a second act for me and you’ve given me that, this industry has given me that and I want to thank you and I’m so grateful and proud.”
Argo was also named best film.
Quentin Tarantino picked up the best original screenplay for his western slavery tale Django Unchained and thanked his actors for doing a “bang-up job with my dialogue”.
The film has attracted criticism for its liberal use of racial insults and Tarantino thanked his backers for standing by what he described as “a hot potato” film.
Lincoln actress Sally Field presented the director with his award without her presenting partner, Les Miserables star Eddie Redmayne, after he was taken ill backstage with suspected food poisoning.
Field told the audience: “He seems to be puking his guts out back there.”
There were more accolades in store for Django Unchained as Christopher Waltz picked up the prize for best supporting actor for his role as bounty hunter Dr King Schultzin the spaghetti western.
Accepting his award from The Hunger Games star Jennifer Lawrence, he said it was an “immense honour” and paid tribute to its “silver-penned” writer.
He said: “Why I get to stand here is really no mystery because it says at the beginning of our film: ‘Written and directed by Quentin Tarantino’.”
The best supporting actress award went to Anne Hathaway for her role as Fantine in Les Miserables.
She thanked the “golden-hearted group” who made the film and wished her co-star Redmayne well, saying: “Feel better. I mean I’d be holding your hair back, but, you know...”
She also thanked Victor Hugo – the writer of the novel that inspired the musical – saying: “Without whom, none of us would be here.”
The 3D adventure epic Life of Pi won the award for best cinematography, which director Ang Lee picked up on behalf of Claudio Miranda. The film, adapted from Yann Martel’s 2001 novel, also won the award for best special visual effects.
Among the other prizes presented last night was an award for outstanding British contribution to cinema to FilmFour boss Tessa Ross.