He thanked Indian actor Suraj Sharma in his acceptance speech, which he ended with a warm "Namaste".
"Life of Pi", an adaptation of Canadian author Yann Martel's Man Booker Prize-winning eponymous novel, narrates the journey of an Indian boy who survives a storm. Widely shot in India, the fantasy adventure drama stars young Suraj in the lead role, with acclaimed Indian actors Irrfan and Tabu playing key parts.
In his acceptance speech, Lee thanked his producers, "Indian crew", Suraj and all technicians who worked on the movie.
"Suraj, where are you?" he said, and the cameras panned to Suraj, a 19-year-old Delhi boy, who made his acting debut with the movie. He waved at Lee with joy.
Others who were vying for the best director's trophy included Steven Spielberg ("Lincoln"), Michael Haneke ("Amour"), Benh Zeitlin ("Beasts of the Southern Wild") and David O. Russell ("Silver Linings Playbook").
Ang Lee had earlier won an Oscar for "Brokeback Mountain" in 2005.
Spotted: Virat Kohli, Anushka Sharma and other celebs at Mumbai airport
Photos: Salman Khan's 'special friend' Iulia Vantur at a song launch
Photos: Hrithik Roshan, Anushka Sharma, other celebs dazzle at event
In Pictures: Sex scandals involving Indian politicians
Photos: Abhishek Bachchan and Farah Khan at Boman Irani's birthday bash