That exchange led to a game deduction for Williams, leaving her trailing 5-3 and clinching the match for Osaka.
It was a shock win for Osaka, playing her first grand slam final against one of the greatest tennis players in the world.
Williams fans in the crowd, angry over her exchange with the umpire, continued to boo.
Osaka had been composed on the court but became clearly emotional after winning, and pulled her visor over her face as Williams put a comforting arm around her.
Ellen Show host Ellen Degeneres asked Osaka what Williams said to her at that moment, and Osaka said Williams was reassuring her.
"She said that she was proud of me and that I should know that the crowd wasn't booing at me, so I was really happy she said that," Osaka said.
"At the time I did kind of think they were booing at me, 'cause I couldn’t tell what was going on because it was just so loud in there, it was just a little bit stressful."
While the match was packed with drama, Osaka told Degeneres she didn't even know what exactly had happened because she was trained as a child not to look when an opponent gets angry.