It comes after the broadcast of a new documentary about Kelly, which detailed allegations of sexual and physical abuse against women and underage girls, spanning several decades.
Gaga called the stories "horrifying" and "indefensible", adding: "I stand behind these women 1000%".
Kelly has denied all the allegations.
His lawyer also dismissed the documentary as "another round of stories" being used to "fill reality TV time".
But film-maker Dream Hampton said the film depicted how Kelly had "built an ecosystem around his predation", after almost three decades of "preying on young and vulnerable women".
Gaga had been under pressure to comment on the allegations against Kelly ever since she collaborated with him on 2013's Do What U Want (With My Body).
The song was controversial from the outset. Stories about Kelly's personal life had already been widely reported and, in 2008, he stood trial on charges of making a sex tape with an under-age female. He was found not guilty.
At a press conference in Japan in 2013, Gaga defended the collaboration, saying: "R Kelly and I have sometimes had very untrue things written about us, so in a way this was a bond between us."
But calls for her to condemn Kelly resurfaced last week, after it emerged she had allegedly declined to be interviewed for the Lifetime documentary.