Daniel Day-Lewis has become the first person to win the best actor Oscar three times for his exactingly authentic performance as President Abraham Lincoln in Steven Spielberg's historical drama.
He has been nominated five times for the Academy Award, winning for My Left Foot in 1990 and There Will Be Blood in 2008.
The 55-year-old spent a year preparing for Lincoln , and, in his customary method, remained in character during the production.
His widely-expected Oscar win further cements his status as the most admired actor currently working.
Taiwan-born Ang Lee won best director for spectacular 3D fantasy Life of Pi.
The other nominees on Sunday night were Bradley Cooper for Silver Linings Playbook , Hugh Jackman in Les Miserables, Joaquin Phoenix for The Master and Denzel Washington in Flight.
Jennifer Lawrence took home the award for best leading actress for her role in Silver Linings Playbook, Christoph Waltz won best supporting actor for his part in Django Unchained and Anne Hathaway was awarded the best supporting actress for her role in Les Miserable .
Winners and losers
Al Jazeera's Rob Reynolds, reporting from Los Angeles, said that political controversy surrounding Zero Dark Thirty, about the CIA's hunt for Osama Bin Laden and the military operation that resulted in the death of the al-Qaeda leader , took a toll on the film.
"The film came under criticism from politicians in Washington, for its scenes involving torture with politicians saying that it gave too high a prominance to torture and implied that the information that led to Bin Laden [being found] was tortured out of captives and detainees."
"So while the film, Zero Dark Thirty, was highly touted and really praised by a lot of critics as a highly polished and compelling film, it won virtually no major awards tonight," said Reynolds.
The 85th Academy Awards took place at the Dolby Theatre in Los Angeles with host Seth MacFarlane.
Iran hostage drama Argo won the Oscar for best film, the top prize at the movie industry's most coveted awards, beating rival Lincoln.
The thriller, which is based on a true story, recounts a CIA mission to rescue six US diplomats from Iran after the 1979 Islamic Revolution, under the cover of making a fake Hollywood film.
Argo won a slew of other Hollywood awards despite its director, Ben Affleck, being left off the Academy Award directing shortlist.