Maher's show, which starts at 12:05 a.m., has aired on ABC since 1997 and started on Comedy Central in 1993.
"Politically Incorrect" was believed to be in trouble ever since Maher, in the wake of the Sept. 11 terrorist attacks, was quoted as referring to past United States military actions as "cowardly." FedEx and Sears pulled their advertising from the show.
ABC Chairman Lloyd Braun said Maher's controversial comments had nothing to do with the decision to replace him.
"We made a decision to go with straight entertainment programming in late-night," Braun said on Tuesday. "That's just basically a scheduling opportunity that we felt over the long-term had more potential."
ABC signaled its intention to get more entertainment in late-night earlier this spring when it tried to get David Letterman to jump from CBS to replace Ted Koppel's "Nightline."
Letterman decided to stay put, and ABC gave "Nightline" a two-year commitment. But the network is still interested in building a late-night entertainment franchise to reach desirable younger viewers.
Kimmel is co-host of Comedy Central's "The Man Show," an unabashed beer-and-babes comedy that revels in being politically incorrect.
Braun said Kimmel's ABC program "is not going to be like 'The Man Show' at all, although Jimmy's Jimmy."
The show is scheduled to premiere in January.
ABC was scheduled to have Kimmel talk about his program to advertisers Tuesday at the network's presentation of next season's schedule.