Sir Kenneth Branagh presented the British monarch with her trophy, which is to recognise her support for the British film industry throughout her reign.
Christopher Nolan, Damian Lewis, George Lucas, James Nesbitt, Tom Hooper and Idris Elba were among the stars who attended the event.
John Hurt, Billy Connolly, Minnie Driver, Rebecca O'Brien, David Hare, Leslie Phillips, Edgar Wright and others were also in attendance.
BAFTA chairman John Willis paid tribute to the Queen, stating: "We should be proud of our industry. The people here this evening represent a vast variety of skills and ground breaking innovation; they have entertained and informed a generation and inspired generations to come."
He added: "I am delighted that this evening has given us the opportunity to give something back. I have the great honour to announce that we are to present Her Majesty with an honorary BAFTA today, in recognition of her outstanding patronage of the film and television industries.
"The Queen has been patron of the Royal Academy of Dramatic Arts, the Entertainment Artistes' Benevolent Fund and the Cinema and Television Benevolent Fund - for which money is raised by Royal Film Performances - since 1952, so for more than 60 years, and visited countless industry organisations, shining a light on the work that we all do and lending her tireless support to our efforts.
"More recently Her Majesty the Queen starred at the London Olympics as the most memorable Bond girl yet."
The Queen BAFTA ceremony in pictures: