Target was supposed to sell a deluxe edition of the album, set to be released in May, with bonus content. But gay advocates expressed their concern about the partnership because of Target's donation to a political candidate who was against same sex marriage.
The Advocate reported Tuesday that Gaga wasn't comfortable with the deal and ended it.
A representative for the singer said Wednesday the two sides "came to a mutual decision to end their overall exclusive partnership a few weeks ago."
Target says it's "very surprised and disappointed" and that it remains committed to the lesbian, gay, bisexual and transgender community.
The Associated Press contributed to this report.