After the candidates finish their two-minute replies, they will be allowed to freely engage with one another for the remainder of the segment. (The debate, to be moderated by Kristen Welker of NBC News, is divided into six segments of 15 minutes apiece.)

Aides to Mr. Biden and Mr. Trump were notified of the change late Monday. Mr. Trump signaled late Monday that he was not happy about it.

Speaking to reporters on Air Force One after a day of campaigning in Arizona, Mr. Trump raised objections to the commission’s plans but confirmed that he would take part in the debate.

“I’ll participate, I just think it is very unfair,” Mr. Trump said. “I will participate, but it’s very unfair that they changed the topics and it is very unfair that again we have an anchor who is totally biased.”