The actor beat out fierce competition from Denzel Washington (Fences), Andrew Garfield (Hacksaw Ridge), Viggo Mortensen (Captain Fantastic) and Ryan Gosling (La La Land) to win the trophy.
While Affleck won the Golden Globe in January, it was Washington who bagged the Screen Actors Guild award earlier this month - an accolade that's correctly predicted the eventual Oscar winner for the past 12 years.
This is the second Oscar for Manchester by the Sea in which Affleck plays Lee Chandler - writer-director Lonergan won Best Original Screenplay for the film earlier in the evening.
More to follow.
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