The freshman power forward was suspended from the team last month after he was charged with two counts of simple assault and harassment following a fight at an off-campus apartment.
He is scheduled to appear in court at a later date.
"I am sorry," Pinkston said in a statement. "This situation is my responsibility and I have learned from it. I am going to work extremely hard so that I can return to the Villanova family in June."
Pinkston, who cannot take classes in the spring, will retain his eligibility since the suspension is a university sanction and not an NCAA penalty. He can return to Villanova in the summer as a redshirt freshman, with four years left to play.
"I am in support of the university's decision," coach Jay Wright said in a statement. "JayVaughn understands that there are consequences to his actions and I believe he will continue to handle this in a mature manner. We look forward to his return in June."
The hefty punishment is in keeping with how the university has handled similar cases.
Last year, senior Reggie Redding was suspended for the fall semester after police found a small amount of marijuana in his car following a minor car accident.
A source said that Pinkston is receiving the same punishment any Villanova student would under similar circumstances.
The loss of Pinkston leaves guard-oriented Villanova short-handed at the power forward spot. A McDonald's All-American out of Bishop Loughlin High School in New York, Pinkston was expected to contribute immediately alongside Mouphtaou Yarou and Antonio Pena.
Dana O'Neil covers college basketball for ESPN.com.