The 45-year-old actor says he acted "inappropriately" towards the 'One Tree Hill' star.
Hilarie Burton received an apology from Ben Affleck on Wednesday after she accused him of groping her while she was a host on MTV's Total Request Live.
"I acted inappropriately toward Ms. Burton and I sincerely apologize," the 45-year-old actor wrote.
The alleged incident came to light on Tuesday after a fan tweeted that Affleck should have "kept quiet" about the Harvey Weinstein sex scandal, given his history with Burton.
"He also grabbed Hilarie Burton’s breasts on TRL once. Everyone forgot though,” the Twitter user wrote.
The 35-year-old actress responded: "I didn't forget."
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"I’m so sorry that happened to you,” the fan replied. “It’s infuriating that people never bring up all the gross, predatory things he’s done."
Burton -- who is currently expecting her second child with her actor husband, Jeffrey Dean Morgan -- tweeted back: "Seriously, thank you for that. I was a kid."
Continuing the Twitter correspondence, the fan wrote: "I remember when that happened and never forgot about it. We see you."
The former One Tree Hill star then tweeted a video of a promo for a TRL special, where she candidly talks about the alleged incident. In the clip, she exclaims, "And then he comes over and tweaks my left boob!"
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Later on in the teaser, Affleck is seen being interviewed by Burton, and asks her, "How old are you, 19?"
"Girls. I'm so impressed with you brave ones," she captioned the promo. "I had to laugh back then so I wouldn't cry. Sending love."
Following news of the alleged groping, a source close to Affleck told ET, "Ben has done things in the past in jest that could be seen as over the top or inappropriate but he would never intentionally hurt or harass anyone."
ET has reached out to both Affleck and Burton's reps regarding these allegations, as well as TRL and Carson Daly, who was the lead host of the show at the time.
Prior to apologizing to Burton, Affleck rebuked Weinstein in a statement, following newly published allegations by multiple women claiming he sexually assaulted them. Meanwhile, the movie producer's spokesperson, Sallie Hofmeister, has denied all allegations that Weinstein had non-consensual sex with anyone.
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"I am saddened and angry that a man who I worked with used his position of power to intimidate, sexually harass and manipulate many women over decades," the 45-year-old actor said of Weinstein. "This is completely unacceptable, and I find myself asking what I can do to make sure this doesn’t happen to others."
Here's a look at how other celebrities have responded to the Hollywood movie mogul's alleged indecent behavior: