Two others were injured in the shooting, which occurred on a bus filled with students returning from a field trip on Sunday evening.
They were attacked as the bus pulled into a parking garage on the university campus, police say.
A suspect is in custody charged with three counts of second degree murder and three counts of using a handgun.
No possible motive for the attack was reported as police continued their investigation.
A shelter-in-place order for the campus has been lifted but classes were cancelled on Monday.
The shooting reportedly took place at around 22:30 (03:30 GMT) at a garage on Culbreth Road, on the university's Charlottesville campus.
Those killed were identified as Devin Chandler, a second-year student from Virginia Beach, D'Sean Perry, a fourth-year student from Miami, Florida, and Lavel Davis, a third-year student from Rich Hill, South Carolina.
A law enforcement car blocked access to the crime scene
Police say the bodies of the victims were found inside a charter bus after they returned from a field trip.
The university named the suspect as one of its students, Christopher Darnell Jones Jr, aged 22.
"I am devastated that this violence has visited the University of Virginia," said Jim Ryan, the university's president.
The university is considered among one of the most prestigious in the country and ranked number three in public universities in the US.