CD and vinyl reissues of the 2013 album no longer include the track "Do What U Want", which featured the embattled R&B star, who is behind bars awaiting trial for a number of sexual assaults.
GaGa has made the physical copies of the revamp available for pre-order via her website. The new release drops on 11 November.
The "Poker Face" singer distanced herself from Kelly in the wake of the "Surviving R. Kelly" documentary, which aired on TV in America in January. The film detailed decades of sexual abuse allegations against the singer.
Earlier this year, she vowed to remove "Do What U Want" from streaming platforms, while apologizing for including Kelly on "Artpop", calling the allegations against him "indefensible".