Johnson was charged Tuesday with having sexual intercourse without consent.
Johnson previously has denied the allegation. Attorney David Paoli released a statement Tuesday that said Johnson and his family "are surprised and saddened" by the timing of the criminal charge. The encounter took place in February and police have been aware of the allegation since the woman, another student, filed a report six weeks later.
"Jordan strongly maintains his innocence and looks forward to the opportunity to prove his innocence at trial, clear his name and return to pursuing his education," Paoli said in the statement.
University president Royce Engstrom said that given the charges, Johnson has been suspended from football team activities, as called for by the student-athlete conduct code.
"In our profession, you have to be prepared to face the unexpected," Montana head football coach Mick Delaney told the Missoulian. "This being the unexpected, we'll make an adjustment."
It's the latest turn in a sexual assault scandal at the university that has prompted three investigations by federal governmental agencies and the NCAA. The Department of Justice and Department of Education are investigating how the university and city officials responded to reports of sexual assault on campus and in Missoula.
A university investigation earlier this year found nine allegations of sexual assault that had gone unreported over 18 months, and two others have surfaced since then.
Some have involved student-athletes, but only those cases involving criminal charges have been made public. In January, running back Beau Donaldson was suspended from the team after he was charged with raping an acquaintance in September 2010. He has pleaded not guilty.
In the aftermath of that report and as the federal investigations became publicly known, Engstrom fired head football coach Robin Pflugrad and athletic director Jim O'Day, saying a change in leadership was needed.
According to Boylan's court documents, Johnson and the female student have known each other since 2010 and they began texting each other regularly in December 2011.
On Feb. 4, they decided to watch a movie together in the woman's room. He then kissed her, pulled her on top of him and tried to take off her shirt, according to the court documents.
When she resisted, he became aggressive, pulled her clothes off and raped her, Boylan wrote in the documents.
Afterward, the woman sent a text to her roommate in the next room that said, "Omg ... I think I might have just gotten raped."
"She has sought counseling and has shown signs of depression, panic and Post-Traumatic Stress Disorder consistent with Rape Trauma Syndrome," Boylan wrote.
Boylan added that Johnson said it was consensual sex and that he broke off communications with the woman afterward because he liked another woman and didn't want that woman to be upset if she knew he had sex with the alleged victim.
Johnson led the Grizzlies to an 11-3 record in 2011 and a share of the Big Sky Conference Title. Montana lost in the semifinals of the Football Championship Subdivision playoffs.
Johnson passed for 2,400 yards and 21 touchdowns last season, his first as a starter.
Johnson is due in court Aug. 14, the Missoulian reports.