Officer Larry Kamholz says Audrey Seiler, 20, has non-life-threatening injuries and was taken to a hospital.
Police say Seiler was found in a marsh near campus.
In a Wednesday evening press conference, authorities said they sealed the area where Seiler was found after reports a suspect armed with a gun and knife may still be in the area.
They said they are looking for a white male in his late 20s or early 30s, approximately six feet tall, wearing a black sweatshirt, jeans and a black cap.
Police with their weapons drawn could be seen walking through the parking lot of a building near the marsh.
The doctor who treated Seiler says she's suffering from muscle aches from being confined, but police are offering few details of their investigation, reports CBS News Correspondent Jennifer Donelan.
"Audrey is doing well and she's happy to be back," her father Keith Seiler said at the evening news conference.
A surveillance tape showed Seiler leaving her building early Saturday, and her door was left open, police said.
Volunteers from Seiler's hometown of Rockford, Minn., slogged through marshes around campus Tuesday, while investigators scoured phone records and searched apartments for any clue into her disappearance.
Madison Police Capt. Luis Yudice had said investigators are trying to determine whether Seiler's disappearance is related to a Feb. 1 attack that left her unconscious when she was struck from behind by an unknown assailant.
Her uncle, Scott Charlesworth-Seiler, said his niece had no idea who may have wanted to harm her and believed the attack was random.
"Audrey was worried after having been attacked and, as a result, was more careful to walk with friends and make sure she was safe," he said.
Volunteers searched the University of Wisconsin Arboretum, a large wooded area south of campus. Police also used search-and-rescue dogs, planes and boats.
Last November, University of North Dakota student Dru Sjodin was kidnapped from a mall parking lot in Grand Forks, N.D. A Minnesota man has been charged with abducting her. She is feared dead, but no body has been found.