Lee's big screen adaptation of Yann Martel's 2001 novel beat Peter Jackson's The Hobbit: An Unexpected Journey, which had looked set to dominate the ceremony with seven nominations but only managed to pick up one for its virtual cinematography.
Life of Pi triumphed in the Outstanding Visual Effects, Outstanding Animated Character, Outstanding FX Simulation Animation and Outstanding Compositing in the live action feature categories.
Lee himself was also honoured with the Visionary Award, in recognition of his use of visual effects throughout his big screen career.
Pixar's animated tale of a Scottish princess, Brave, swept the animated categories by winning trophies for Outstanding Animated Character, Outstanding Created Environment, Outstanding Animation, and Outstanding FX Simulation Animation.
Oscar-winning special effects cinematographer Richard Edlund, who worked on the original Star Wars series, was presented with the Lifetime Achievement Award at the event at the Beverly Hilton hotel in Los Angeles.