In a letter of resignation sent to university president Robert Barchi, Pernetti said he hoped that his tenure at Rutgers "will not be judged by this one incident."
When he first saw the video of former coach Mike Rice pushing, shoving and throwing balls at players in November, Pernetti said he wanted to fire him on the spot. However, he said the consensus among school officials at the time was the actions didn't call for dismissal.
The video was broadcast Tuesday on ESPN, showing numerous clips of Rice at practice firing basketballs at players, grabbing them by their jerseys and yelling obscenities in addition to gay slurs.
At a news conference on campus, Barchi said he regretted not asking to see the video when Pernetti first told him of its existence.
"I want to apologize to the entire Rutgers community for the negative impact that this situation has had on Rutgers," Barchi said.
Pernetti said in his resignation letter to Barchi that he has "spent a great deal of time reflecting on the events which led to today. As you know, my first instincts when I saw the videotape of Coach Rice's behavior was to fire him immediately. However, Rutgers decided to follow a process involving university lawyers, human resources professionals, and outside counsel.
"Following review of the independent investigative report, the consensus was that university policy would not justify dismissal. I have admitted my role in, and regret for, that decision, and wish that I had the opportunity to go back and override it for the sake of everyone involved," it said.
Pernetti was given the video in late November by a former employee, Eric Murdock. With Barchi's approval, he suspended Rice for three games, fined and docked him pay totaling $75,000 and ordered him to attend anger management classes.
Barchi said Friday he did not see the video until this week, clearing up a discrepancy as to when he first viewed it.
The 42-year-old Pernetti is a Rutgers graduate who played tight end for the Scarlet Knights from 1989-93.
Before Pernetti's resignation, there was an outcry from Rutgers faculty and state legislators not only for his ouster but for Barchi's as well.
By Friday morning, nearly 3,000 people had joined a Facebook site calling for the university to keep him, several accusing the media and politicians of a witch hunt. Former Rutgers football players including Baltimore Ravens running back Ray Rice and Eric LeGrand, who was paralyzed during a game in 2010, were among those campaigning for Pernetti.
On Thursday, assistant coach Jimmy Martelli resigned.
Pernetti's finest hour may have been when he helped in the school's move to the Big Ten Conference, which means millions in additional revenue by way of television contracts and more national exposure, especially in football. The move, which becomes official in 2014, should provide a big boost to the program in recruiting and season ticket sales. The Scarlet Knights will continue to play next season in the Big East.
Pernetti's first major move as athletic director came in May 2010, when he hired the volatile Mike Rice away from Robert Morris, which he took to two NCAA tournament appearances.
"He convinced me he understood his reputation, but he also understood where the line was," Pernetti said, referring to Rice. "I made clear to him if he crossed the line he would be held accountable."
The move might have been too soon for a coach like Rice, and clearly Pernetti took a serious risk. After all, most Big East coaches do not land there immediately after stops in the Northeast Conference, but Rutgers and Pernetti looked at Rice and saw the man who could turn around the perennially underachieving program.
It never happened. Rice went 44-51 in three years and posted a 16-38 mark in the Big East after going 73-31 in three seasons at Robert Morris. The Scarlet Knights went 15-16 this season, including 5-13 in the league, and questions about Rice's status — based on wins and losses alone — began to surface.
But Pernetti again made a questionable decision. Given what he knew about the video, and taking Rice's record into consideration, he still gave the coach a public endorsement at season's end.
"Of course he's coming back," Pernetti said at the time. "It's been an interesting year to say the least, and while I think in one case some of the progress — and there's been a lot of progress — doesn't show, and that's in the win-loss column. I would like it to show there. I think everyone in the program would. But you can definitely see us getting better."