Making an unprecedented appearance from White House through a video link, First Lady Michelle Obama helped actor Jack Nicholson present the final prize.
"I want to acknowledge the other great films that have as much right to be up here as we do and many of them who did not even get nominated this year," Affleck, 40, said as he sped through his speech.
Taiwan's Lee upset front-runner Spielberg to win his second Best Director Oscar for visually stunning 3D survival tale of an shipwrecked Indian boy lost in the ocean with a Bengal tiger.
"Thank you, movie god. Everybody who worked with me on Life of Pi. I want to thank you for believing in this story and share this incredible journey with me... Wonderful cast. Suraj, where are you? You're a miracle... Thank you, Xie xie, namaste," Lee said.
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British actor Daniel Day-Lewis, 55, created history by winning his third Best Actor Oscar for bringing to life the 16th US President Abraham Lincoln in 'Lincoln'. His previous wins were for 'My Left Foot' in 1989 and 'There Will Be Blood' in 2007.
"I've received so much more than my fair share of good fortune in my life... At the apex of that human pyramid there are three men to whom I owe this and a great deal more: Tony Kushner, our beloved skipper Steven Spielberg and the mysteriously beautiful mind, body and spirit of Abraham Lincoln," said Day-Lewis in a gracious speech, acknowledging fellow nominees as "my equals, my betters".