Scott added 10 rebounds and three blocks. Joe Harris contributed 19 points on 7-of-9 shooting for the Cavaliers (18-3, 5-2 ACC).
Clemson's Tanner Smith made a 3-pointer with 13 seconds left to get the Tigers to within 63-61, but Scott sealed the win with two free throws.
Akil Mitchell provided eight points and seven rebounds as Virginia registered its third straight win following a Jan. 22 loss to Virginia Tech.
Smith finished with 14 points for the Tigers (11-10, 3-4).