Kimmel said he had thought of his performances as "impersonations of celebrities and nothing more".
But, looking back, he admitted they were "embarrassing" and described them as "thoughtless moments".
He said sorry "to those who were genuinely hurt or offended by the make-up I wore or the words I spoke".
Kimmel fronts a late-night talk show on ABC and hosted the Oscars in 2017 and 2018.
He had been under pressure to address his past use of blackface, especially after fellow presenter Jimmy Fallon issued a similar apology last month.
It has also just been revealed that Tina Fey asked for four episodes of sitcom 30 Rock in which characters appear in blackface to be taken down.