DeGeneres said the abuse took place when she was 15 or 16, after her mother was diagnosed with breast cancer.
"He told me... he'd felt a lump in her breast and needed to feel my breasts," she told interviewer David Letterman.
DeGeneres first spoke about the abuse in 2005, but said she was now going into more detail "because I want other girls to not ever let someone do that".
Speaking on Letterman's Netflix show My Next Guest Needs No Introduction, the 61-year-old explained that her late former stepfather had first assaulted her when her mother was out of town, telling her he needed to check for lumps.
"I didn't know about bodies. I don't know that breasts are all different," she said.
"Anyway, he convinced me that he needs to feel my breasts and then he tries to do it again another time, and then another time he tries to break my door down and I kicked the window out and ran 'cause I knew it was going to go more to something."
The comedian said she did not tell her mother at first because she didn't want to upset her.
"I should never have protected her," she said. "I should've protected myself, and I didn't tell her for a few years and then I told her, and then she didn't believe me and then she stayed with him for 18 more years."
DeGeneres explained that her mother did ultimately leave her husband after he kept changing his version of events. The TV star hopes other young girls will benefit from hearing her tale.
"That's the only reason I think it's important to talk about it," she said. "Because there's so many young girls and it doesn't matter how old you are.
"When I see people speaking out, especially now, it angers me when victims aren't believed, because we just don't make stuff up.
"And I like men, but there are so many men that get away with so much."