The 9,000-word story, published on November 19, prompted student protests and the suspension of fraternities at the University of Virginia, while rekindling a national debate about sexual violence on American college campuses.
Unusually, at the request of her subject, a first-year student identified only as Jackie, journalist Sabrina Rubin Erdely never contacted the men who allegedly took part in the gang rape during a frat house party.
"In the face of new information, there now appear to be discrepancies in Jackie's account, and we have come to the conclusion that our trust in her was misplaced," the magazine said on its website.
"We were trying to be sensitive to the unfair shame and humiliation many women feel after a sexual assault and now regret the decision to not contact the alleged assaulters to get their account."
The full story nevertheless was still visible on Rolling Stone's website, preceded by the statement from managing editor Will Dana.
She also posted messages on her Twitter account explaining her decision.
Student reporter Catherine Valentine at the University of Virginia, said she feared that the magazine's apology could have chilling effect on rape survivors coming forward with their stories.
"I'm worried that girls are not going to report now out of fear of being called liars," Ms Valentine told CNN.
In the wake of the magazine's apology, social media users posted messages of support for Jackie using the hastag #IStandWithJackie.
The University of Virginia is among nearly 90 US colleges now under federal investigation for allegedly mishandling sexual violence complaints.
President Barack Obama has highlighted the scourge of sexual assault on US college campuses.
In September, he noted that an estimated one in five women in the United States have been sexually assaulted during their college years, yet only 12 percent of cases are reported.
Rolling Stone's climbdown came as Phi Kappa Psi, the nationwide fraternity whose members purportedly carried out the gang rape, issued a statement rebutting Jackie's version of the events.
It claimed it hosted no party on the weekend Jackie said she was attacked, and that none of its members fit the description of her prime assailant, a student named Drew.
"No ritualized sexual assault is part of our pledging or initiation process," the fraternity added. "This notion is vile, and we vehemently refute this claim."
The Washington Post said it has interviewed Jackie "several times" in the past week, and that the 20-year-old -- still a University of Virginia student -- "stands by her version of the events."
"What bothers me is that so many people act like it didn't happen. It's my life. I have had to live with the fact that it happened every day for the last two years," it quoted Jackie as saying.
No charges have been laid in the alleged gang rape, which the University of Virginia -- founded by Thomas Jefferson in 1819 -- has put under investigation.
Share
