The story created an uproar at the school and prompted renewed U.S. debate on sexual abuse. The fraternity, Phi Kappa Psi, rebutted key parts of the Rolling Stone story on Friday.
The story, by reporter Sabrina Rubin Erdely, described a 2012 alleged attack on a woman named Jackie at a Phi Kappa Psi fraternity house pledge party and the university's alleged failure to respond to the attack.
In a note to readers posted on the magazine's website, Rolling Stone Managing Editor Will Dana said new information showed that there were "discrepancies" in Jackie's account of the alleged rape by seven men.
"We have come to the conclusion that our trust in her was misplaced," Dana said.
"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. We are taking this seriously and apologize to anyone who was affected by the story," Dana said.
The magazine has identified the accuser only as Jackie, her real first name.
The fraternity's University of Virginia chapter, in a statement, pointed out inconsistencies in the story. It said Phi Kappa Psi did not hold a party on the weekend of Sept. 28, 2012, the night of the alleged attack. And it said that pledging and initiations take place only in the spring semester, not in the fall.
In addition, no members of the fraternity were employed at the university's Aquatic and Fitness Center at the time, as Erdely reported, the statement said.
The magazine article said that Jackie had met one of her alleged attackers, who she said was a fraternity member, while they both worked as lifeguards at the university's pool.
Erdely could not be reached immediately for comment via phone or email. On her own web page (www.sabrinaerdely.com) Erderly describes herself as "an award-winning feature writer and investigative journalist," as well as a contributing editor at Rolling Stone.
Phi Kappa Psi said it was working with Charlottesville police as officers investigate allegations in the article. Charlottesville police spokesman Captain Gary Pleasants said the investigation was ongoing.
Rolling Stone's Dana said that the magazine, at Jackie's request, had not contacted the man she claimed orchestrated the attack nor any of the men she claimed took part because of fear of retaliation against her.
In a Tweet, Dana said: "We made a judgment – the kind of judgment reporters and editors make every day. And in this case, our judgment was wrong."
Rolling Stone was founded in 1967 by Jann Wenner, who still owns and operates it, along with US Weekly and Men's Journal.
University President Teresa Sullivan said in a statement that since the Rolling Stone article two weeks ago, the school had been centered on the issue of sexual violence on college campuses.
The magazine's apology left that focus unaltered and the school would continue to examine its policies and procedures, she said.
The story, along with allegations of sexual abuse against comedian Bill Cosby, galvanized the U.S. debate on sexual assault, especially on college campuses. The U.S. Department of Education is investigating sexual violence cases at 90 colleges and universities.
The Rolling Stone story prompted protests over sexual abuse at the school, and the fraternity was vandalized. Sullivan suspended fraternity and sorority activities until Jan. 9, and the university chapter of Phi Kappa Psi surrendered its fraternity agreement with the school and suspended activity.
Sullivan also announced stepped-up policing and alcohol measures in light of the article, and the school's trustees held a special meeting to discuss it.
Virginia Attorney General Mark Herring in a statement called Rolling Stone's apology "deeply troubling" since the magazine was not correcting the story. Herring has appointed an independent counsel to examine the allegations and how the school handled the matter.
In an email, Tom Mullen, director of public affairs journalism at the University of Richmond, called the story "an epic failure on the part of Rolling Stone."
"What victim will now want to come forward, and at what cost?" he said.
Fraternities and sororities are social clubs common at many U.S. colleges and often have their own housing. Many of the University of Virginia's 21,000 students are affiliated with the so-called Greek system.
While the issue of sexual abuse on U.S. college campuses has been a growing issue, there have also been cases of rape accusations that have proved unfounded.
Three lacrosse players at Duke University who were charged in 2006 with sexual assault were declared innocent after the accuser's story was discredited.