The singer revealed that she made the song during a very dark time in her life and referred to her thinking around its production "explicitly twisted".
She said she should have sought therapy or other help instead.
Since the Lifetime series's January 3 premiere, a number of celebrities have publicly denounced Kelly, but many noticed that Gaga, who revealed in 2014 that she was a survivor of sexual assault and is a vocal supporter of the #MeToo and Time's Up movements, was not among them.
The singer recently spoke out on the allegations R.Kelly is now facing and apologized for ever working with him.
The singer has previously been subject of sexual impropriety allegations and, in 2008, stood trial on child pornography charges, of which he was acquitted.
Gaga had come under scrutiny in 2013 when she chose to collaborate with Kelly, despite his alleged history of sexual misconduct, performing the song together at the American Music Awards that same year. Gaga's comments come after release of a documentary over R Kelly.
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Read the full statement below. "We fully support all victims of sexual abuse, and it's our hope that there will be a path to justice".
Kelly, 52, has denied the accusations lobbed against him and his lawyers have threatened to sue Lifetime over the docuseries, according to Insider.
Gaga is not the only celebrity to distance herself from Kelly.
Ever since then-27-year-old R Kelly married 15-year-old Aaliyah in 1994, his alleged abuse of young black girls has been an open secret.
"I´m sorry, both for my poor judgment when I was young, and for not speaking out sooner", she posted on Twitter.
John Legend, the only big star to appear in the documentary, was unfazed by the praise he's been getting for his bravery. "That we were able to say, the public, they can have our bodies, but they cannot have our mind or our heart".
"I wasn't willing to admit that anything had happened", she told Stern, adding, "I didn't tell anybody".
In response to the positive feedback he received as a result, he tweeted: "To everyone telling me how courageous I am for appearing in the doc, it didn't feel risky at all... You are a attractive person, with a handsome soul that has saved and inspired so many people".