"Life of Pi" was nominated for 11 Oscars - including Best Picture - and also won for Cinematography, Original Score and Visual Effects. Starring newcomer Suraj Sharma, the film was lauded by critics for Lee's ability to bring the complex book to life.
"Thank you movie god," Lee said to a big laugh from the audience.
"I really need to share this with all 3,000 - everybody who worked with me on 'Life of Pi'," he said.
Lee won in a year in which the director's race was one of the most controversial for its exclusions, most notably Ben Affleck, the director of "Argo" who picked up the top award from his peers at the Directors Guild and a slew of other awards.
Lee, 58, won his first Academy Award in 2006 for directing "Brokeback Mountain," the story of a complex love affair between two men.
He began directing Chinese-language films and has made 13 films in a diverse career. Those films have included the special effects-laden "Hulk" based on a Marvel comic Book and the adaption of Jane Austen's classic, "Sense and Sensibility."
His 2000 Chinese-language film "Crouching Dragon, Hidden Tiger," won the Academy Award for Best Foreign Language Film and was a surprise hit with worldwide ticket sales of $213.5 million.
Lee came to Hollywood's attention after directing three Chinese-language films, including "The Wedding Banquet" in 1993, nominated for the Best Foreign Language Film Oscar.
Lee cast Sharma, then a 17-year old student, for the role of a young Pi Patel in 2010 after 3,000 young men auditioned for the lead role.
After his family goes down in the giant ship, Pi spends most of the film on the lifeboat in the middle of the Pacific, trying to avoid being consumed by the 450-pound (200-kg) tiger, a premise that Lee pulled off with heavy reliance on special effects and a digital tiger. The ocean scenes were filmed in a 1.7-million-gallon (6.4-million-liter) tank.
Movie reviewer critic Roger Ebert gave the film 4 out of 4 stars, calling it "a miraculous achievement of storytelling and a landmark of visual mastery."
President Barack Obama also gave "Life of Pi" a thumbs up in an interview with People Magazine, saying the film "was good - because we had read that book together."