The Oscar-winning filmmaker took home 'Best Picture' and 'Best Director' for the movie about the manhunt for Osama bin Laden, while Greig Fraser won 'Best Cinematographer' for the project.
Steven Spielberg's Lincoln also secured three awards, with Daniel Day-Lewis winning 'Best Actor' for his role as the 16th President of the United States.
Sally Field was named 'Best Supporting Actress' for playing Mary Todd Lincoln and Tony Kushner took home the 'Best Screenplay' prize.
The ceremony, which was held today (December 3), is seen as the first major movie awards in the run-up to the Oscars, which take place on Sunday, February 24, 2013, hosted by Seth MacFarlane.
Winners in full:
Best Picture: Zero Dark Thirty
Best Actor: Daniel Day-Lewis, Lincoln
Best Actress: Rachel Weisz, The Deep Blue Sea
Best Director: Kathryn Bigelow, Zero Dark Thirty
Best Screenplay: Tony Kushner, Lincoln
Best Supporting Actor: Matthew McConaughey, Magic Mike and Bernie
Best Supporting Actress: Sally Field, Lincoln
Best Animated Film: Frankenweenie
Best Cinematographer: Greig Fraser, Zero Dark Thirty
Best First Film: How to Survive a Plague
Best Foreign Film: Amour
Best Non-Fiction Film (Documentary): The Central Park Five
Watch the Zero Dark Thirty trailer below: