The 36-year-old said he "keeled over" in front of the crew after filming a scene where he had to violently attack a young slave girl.
The hotly-tipped movie directed by Steve McQueen also stars Brad Pitt but the Kerryman said he was deeply affected by this particular scene.
"That was a kind of strange one," Michael said. "I just blacked out...that has never happened to me. You are doing things that are quite challenging. I guess mentally and physically," he told Elle magazine.
Fassbender plays plantation owner Edwin Epps who delights in abusing slave girl Patsey, who is played by 30-year-old Kenyan actress Lupita Nyong'o.