University President Robert Barchi announced Pernetti's resignation at a news conference Friday, three days after a video showing the abuse was made public, triggering outrage among Rutgers' fans, students and faculty.
Barchi described the resignation as a "mutual decision" and said Pernetti "always had the good of Rutgers and its student athletes in mind in every decision he made, including his decision today."
"I respect and accept Tim's decision to step down and I sincerely wish him well," Barchi said.
The state's largest public university with about 58,000 students has been under fire since Tuesday, when the ESPN sports network released video showing Rice, the men's basketball coach, shoving players, throwing balls at their heads and berating them with homophobic slurs and profanity.
The school fired Rice on Wednesday.
Rice's ouster, and the resignation of Assistant Coach Jimmy Martelli, did little to assuage public anger. On Thursday, 31 faculty members called for Barchi to resign from the president's post and New Jersey state assembly Speaker Sheila Oliver called for public hearings.
Faculty members charged in a letter that Barchi had hidden facts about Rice for months, and acted only after the videos became public.
Ralph Izzo, chairman of Rutgers University's board of governors, defended Barchi's handling of the situation on Friday and told reporters he believed Barchi was "the right person to run this place for many years to come."