Virginia's defense also came through a couple of different times with key goal line stands to stop other potential scoring drives.
The Cougars had a first-and-goal from the 4-yard line but Darren Handley dropped a would-be touchdown pass on third down.
Virginia boosted its lead to 22–9 with 11:17 left in the game when John Ford hauled in a 22-yard pass from Secules and the Cavs had a successful two-point conversion.
The Cougars answered with a one-yard touchdown pass from Sean Covey to Whittingham that made it 22–16 with 7:09 remaining.
BYU had one last shot at a go-ahead touchdown in the final minutes, but Covey was stopped two feet short on a fourth-down run by defensive end Sean Scott.