The accusation was made after the two-time Super Bowl champion spent Thursday night bar hopping with his friends and a group that included the alleged victim, cops said.
"He's been identified as being at the scene and there are allegations naming him as the perpetrator," Deputy Chief Richard Malone said of the Steelers star.
Malone said the quarterback was with three friends when they began mingling with the accuser and a group of her friends. Before the alleged attack, Roethlisberger and the woman visited "multiple establishments" together, Malone said, according to the Atlanta Journal Constitution.
The incident happened at the Capital City nightclub in downtown Milledgeville, a town about 85 miles southeast of Atlanta. The woman told police she was "sexually assaulted or sexually manipulated" by a man whom she described, but did not name Roethlisberger.
"He's been identified as being at the scene," Malone said. The woman was treated and released from a local hospital and has been interviewed by cops. The AJC identified her as a student at Georgia College & State University.
Roethlisberger, who owns a home in the area, also spoke with cops but no charges have been announced. His agent denied the accusation -- while making reference to a prior claim of sexual misconduct against the player.
Roethlisberger, 28, has been sued by a woman who claims he raped her in 2008 at a Lake Tahoe hotel. The Steelers star denies those allegations and has asked for counter-damages.
"Last night, Ben and his friends met a group of women and everyone mingled together throughout the evening," the player's agent, Ryan Tollner, said in the statement.
"We have spoken to law enforcement. Based on information currently available, an allegation was made against Ben, which appeared to be dismissed after a preliminary investigation last night. Obviously, given the prior accusation against Ben, we are skeptical of motive, but we will continue to cooperate with everyone involved."
Steelers spokesman Dave Lockett released a statement from the team. "We are gathering information and that is the only comment we have at this time," it said.
The owner of a restaurant near the nightclub said the quarterback and his friends were at his eatery earlier Thursday night and appeared to be well behaved and friendly.
"He was very polite with everybody," said Frank Pendergrast, owner of The Brick. "He was down here from about 11:30 until about 1:30 having a good time, talking to a lot of people. Looked like he was signing autographs and letting people take pictures. Other than that, it was really uneventful."