Gaga promised on Twitter Wednesday that the track would be removed in response to the multiple sexual assault allegations that Kelly is facing.
Official music videos for "Do What U Want (With My Body)" were also removed from YouTube, however, a video of Gaga and Kelly performing the song at the American Music Awards remains.
"Do What U Want (With My Body)" reached the Top 20 chart on iTunes after Gaga tweeted her intentions and before it was removed.
"I stand behind these women 1000%, believe them, know they are suffering an in pain, and feel strongly that their voices should be heard and taken seriously," Gaga said previously. "What I am hearing about the allegations against R. Kelly is absolutely horrifying and indefensible.
"I'm sorry, both for my poor judgment when I was young, and for not speaking out sooner. I love you," she continued.
Lifetime recently aired a documentary series titled Surviving R. Kelly that chronicled the assault allegations against Kelly. The series featured Kelly's ex-wife Andrea Lee, former underage partner Lizzette Martinez and former backup singer Jovante Cunningham speaking out.