Another comic on the bill for the Comedy Cellar's Sunday night line-up, Mo Amer, said that C.K. was greeted warmly with an ovation from the sold-out crowd.
"It was like a wow moment [for the audience]," he told the Times.
The beloved world-famous comic had a fall from grace when it was revealed he repeatedly masturbated in front of a number of his female associates.
Five women last November came forward about the inappropriate behaviour to the New York Times. The bombshell confirmed years of unsubstantiated rumours about C.K. masturbating in front of associates.
The comedian has admitted to engaging in sexual misconduct.
A Chicago comedy duo, Dana Min Goodman and Julia Wolov, alleged they were invited to his hotel room for a nightcap during a 2002 Colorado comedy festival. The pair assumed the meeting would be "collegial."
Once inside his hotel room, the women said C.K. asked if he could take out his penis. They laughed it off as a joke.
"And then he really did it," Goodman told the New York Times.
"He proceeded to take all of his clothes off, and get completely naked, and started masturbating."
The pair described being "paralysed" from shock, and both fled the room after C.K. had ejaculated.
A year later, comedian Abby Schnacher called C.K. to invite him to one of her stand-up sets, and said she could hear him masturbating during the phone call.
Another woman, who spoke on condition of anonymity, said that C.K. repeatedly asked her to watch him masturbate when they were both working behind the scenes of The Chris Rock Show in the late 90s.
In her early 20s at the time, she went along with his behaviour but says "it was something that I knew was wrong."
The woman "described sitting in Louis C.K.'s office while he masturbated in his desk chair during a workday, other colleagues just outside the door."
Another comedian, Rebecca Corry, said C.K. asked her if he could masturbate in front of her while they were both appearing in a 2005 TV pilot. When she angrily declined, reminding him that he had a daughter and pregnant wife, Corry says C.K. sheepishly told her he had "issues."
In a long statement addressing the claims, C.K. confirmed the accusations and expressed remorse for his actions.
"These stories are true." he wrote.
"The power I had over these women is that they admired me. And I wielded that power irresponsibly. I have been remorseful of my actions … There is nothing about this that I forgive myself for."
The actions resulted in the end of a production deal C.K. had with FX Networks and the cancellation of a movie release for the already controversial I Love You Daddy.
"I have spent my long and lucky career talking and saying anything I want. I will now step back and take a long time to listen. Thank you for reading," the comedian wrote at the time.