The agreement carries no possible state prison time for the 20-year-old Masina, but he could be sentenced to three years in county jail and probation.
Prosecutors haven't decided what sentence they'll seek at a hearing in December, prosecutor Donna Kelly said.
Masina won't be listed as a sex offender.
Defense attorney Greg Skordas said the plea gives his client a chance to "pick up the pieces" at some point.
His accuser's attorney Bethany Warr said the guilty pleas to three counts of sexual battery are "grossly disproportionate" for what she called a violent sexual assault.
The agreement was the best prosecutors could do after Judge Keith Kelly excluded key evidence, she said.
"Their case has been gutted, essentially," she said.
The case is among a series of sex abuse prosecutions across the country involving collegiate athletes that have brought calls for stronger protections by universities and justice systems for women.
Masina was a standout player at Brighton High School outside Salt Lake City, and a sophomore linebacker for USC when he was suspended.
He declined to comment after the hearing. Skordas said he's not expecting Masina to return to USC's team after the case is finished but hopes he can continue his education.
A lawyer for the Masina family, Gregory Phillips, blasted the decision to file charges in the case, saying Thursday there had been a "rush to judgment" against a high-profile athlete.
Masina was initially charged with rape and two counts of forcible sodomy, all felonies. The woman testified that Masina assaulted her after edible marijuana and alcohol left her nearly unable to move at a July 2016 party in the Salt Lake City suburb of Cottonwood Heights.
Skordas said his client believed the encounter was consensual but didn't take into account the woman's clear impairment.
Prosecutors in Los Angeles declined to file charges after authorities investigated allegations that Masina and a USC teammate assaulted the same woman in California days earlier.
Prosecutors said it would be difficult to prove the woman was too intoxicated to consent.