Aiken covered Ripa's mouth with his hand during an interview on Friday's show. Ripa, 36, pushed his hand away.
"Oh, I'm in trouble," said the 27-year-old "American Idol" star, to which Ripa responded, "No, I just don't — I don't know where that hand's been, honey."
O'Donnell said Tuesday on "The View": "If that was a straight man, if that was a cute man, if that was a guy that she didn't question his sexuality, she would have said a different thing."
Ripa said O'Donnell misunderstood her remark.
"He's shaking hands with everybody in the audience. I mean, it's cold and flu season. That's what I meant," she said. "And to imply that it's anything homophobic is outrageous, Rosie, and you know better."
"I understand cold and flu season," O'Donnell replied. "I'm just saying from where I sit as a gay person in the world, I have to tell you, that's how it came off to me."
Aiken has been the target of speculation about his sexuality. Tabloid reports earlier this year suggested he had a gay affair. Aiken has never directly addressed the rumors.
Roger Widynowski, Aiken's spokesman at RCA Records, declined comment on the Ripa-O'Donnell flare-up when contacted by The Associated Press.
On Wednesday's "The View," Walters said, "Rosie O'Donnell is one of the kindest, most sensitive people I know. And so is our friend Kelly Ripa. And Rosie and Kelly talked yesterday after the show. Rosie and Clay Aiken have talked. And all is well with the world, and all is well with them."
Walters said her speech was unrehearsed and that O'Donnell was unaware she was going to say something.