His case has unfolded against a backdrop of NCAA and federal investigations of the university's athletic department and the manner in which rape allegations are handled on campus, investigated by police and prosecuted by the Missoula County attorney's office.
The situation left some worried that the highly successful football team was out of control off the field.
In closing statements Friday, Assistant Attorney General Joel Thompson told jurors that the accuser "has had to crawl through a proverbial tunnel of sewage" to see the case through to trial because she wanted accountability, the Missoulian reported. He alleged Johnson maliciously assaulted his client, resulting in psychological damage.
The female student testified that she and Johnson were kissing at her home last February when his demeanor changed and he held her down and raped her, despite her protests.
Witnesses testified that she was pale and shaking, and that she cried uncontrollably after driving Johnson back to his house.
But Johnson told jurors the sex was consensual and that the woman enjoyed it. He testified that she asked him if he had a condom and when he said he didn't, she told him that was OK. He said she never said "no," and he would have stopped if she had.
The defense argued the woman became upset and sought vengeance after Johnson got up without any cuddling and didn't talk to her other than to say, "Well, thanks," when she dropped him off at his house.
After the verdict was read, Johnson hugged his attorneys and then his large group of supporters in the courtroom.
Asked for comment, Paoli said: "Feel wonderful. Very happy."
Those in attendance Friday included Montana football players, coach Mick Delaney and former athletic director Jim O'Day.
Johnson, who is from the Eugene, Ore., area, was briefly suspended from the football team when the allegations surfaced. He was then kicked off the team under the school's student-athlete conduct code, after the felony charge of sexual intercourse without consent was filed against him in July. He has remained in school.
UM athletic director Kent Haslam said Friday student-athletes can appeal their suspension if there is a change in the circumstances that led to it. Johnson's acquittal would qualify as such a change. Haslam said he has not talked with Johnson about whether he would appeal.
Johnson's trial began with jury selection Feb. 8. District Judge Karen Townsend initially called 400 potential jurors for the high-profile case and eventually seated 12 with five alternates.
Concerns about the handling of sexual assault cases peaked in December 2011, when UM President Royce Engstrom ordered an outside investigation after two students reported being drugged and raped.
Former state Supreme Court Justice Diane Barz later said her investigation found nine alleged rapes or sexual assaults involving students had occurred between September 2010 and December 2011, including at least two that hadn't been reported. One led to former Montana football player Beau Donaldson pleading guilty to rape and being sentenced to 10 years in prison.
Engstrom said in January the investigation "indicated an association with patterns of behavior from a small number of student-athletes."
"We will not tolerate the tarnishing of the proud tradition of Grizzly athletics," he said at the time.
Barz suggested training faculty and staff on how to handle and report sexual assault allegations and rewriting student and student-athlete conduct codes.
Weeks later, the university came under more criticism after the dean of students notified a Saudi national about sexual assault and rape allegations made against him. The student fled the country before the alleged victims could file a police report.
Johnson's case surfaced March 9, when the female student obtained a temporary restraining order against him. He was briefly suspended from the football team, then reinstated when a civil no-contact order replaced the restraining order.
Three days after coach Robin Pflugrad welcomed Johnson back, and touted the "character and tremendous moral fiber" of the player he had known since Johnson was a boy, Engstrom announced he was not renewing the contracts of the coach or O'Day. Both were immediately relieved of their duties, with no explanation from Engstrom.
The move came after a season when Montana advanced to the Football Championship Subdivision semifinal game. The Grizzlies have advanced to the national title game seven times since 1995, winning twice
Last April, the federal Department of Education announced it was investigating a complaint alleging the university discriminated against female students, faculty and staff by failing to address a sexually hostile environmental caused by its failure to appropriately respond to reports of sexual assault.
Soon after, the U.S. Justice Department announced its investigation into the handling of rape investigations and prosecutions, and the school announced in May the NCAA had been investigating its athletic programs since January 2012 for undisclosed reasons. Those investigations continue.