The former PBS anchor said last week's confrontation, viewed by 67 million people, will be remembered as a watershed moment because it was a real debate instead of simultaneous interviews of the candidates.
He took some heavy criticism on social media for his light hand, letting the candidates talk and generally asking open-ended questions designed to encourage them to explore differences.
It was a new format approved over the summer by the Commission on Presidential Debates. Lehrer said the differences were not explained well to the public in advance. The commission issued a statement Friday backing Lehrer.
"I may be seeing something that's not there, but I can't imagine emerging from this experience - I'm talking about myself - with any permanent scars," said Lehrer, who has moderated 12 presidential debates since 1988. "I'm very upbeat about it, and I don't have any second thoughts."
Lehrer planned to divide Wednesday's debate into 15-minute sections divided by topic areas. But that quickly went off the rails.
"The first few times I said 'let's move on' and they wanted to keep talking, the inclination of course is to stop them so I could cover all the subjects I wanted to cover," he said. "But I'm sitting there thinking, 'Wait a minute, they're talking to each other, leave 'em alone.' So I backed off."
He'd get much harsher criticism if he prematurely stopped discussions, he said.
"Not only that, but I would have deserved it," he said.
"It would have been different if they were talking about tiddlywinks or baseball, their favorite color or something like that," he said. "They were talking about the things that really matter."
He said he was surprised to get criticism from political pros and fellow journalists, people he said should have seen what he was trying to accomplish. Among the critics were Dan Abrams of ABC News, Michael Tomasky of The Daily Beast and Rachel Maddow of MSNBC.
"I was thinking, 'Weren't you paying attention to what was happening before your very eyes?'" he said.
Lehrer, who wrote a book last year about his experience moderating presidential debates, characterized the complaints against him as a thunderstorm that is passing. CNN's Candy Crowley and Bob Schieffer of CBS News will moderate the next two Obama-Romney debates. Thursday's vice presidential debate between Joe Biden and Paul Ryan will be run by Martha Raddatz of ABC News.
Lehrer will be 82 during the 2016 presidential election campaign. He said he can't imagine being asked again to moderate and, given the pressure it puts his family through, can't imagine accepting if he were.