Missing eight players -- including four starters -- who were serving one-game suspensions for violating a team rule, the Wildcats (6-4, 4-3 Colonial Athletic Association) guaranteed coach Andy Talley his 17th winning season in 23 years at Villanova.
Towson (3-7, 1-6), which lost its fourth straight game, was limited to 27 yards rushing. Sean Schaefer was 22-for-36 for 242 yards and a touchdown, the 50th of his career.
Whitney, who went 16-for-21 for 116 yards, rebounded from a shaky first half to direct two time-consuming second-half scoring drives for the Wildcats' third win in four games. Villanova held the ball for nearly 39 minutes.
With Towson up 3-0, Whitney moved Villanova 68 yards on 14 plays before Aaron Ball's 2-yard touchdown run off right tackle with 7:52 left in the third quarter.
After Towson's Mark Bencivengo hit a 28-yard field goal to make it 7-6, Whitney converted three third downs in a 13-play, 71-yard march culminating in a 10-yard TD pass to Atkinson on a crossing pattern with 12:01 remaining.
Late in the fourth quarter, Schaefer needed only five plays to move Towson 66 yards, cutting the lead to 14-12 on a 7-yard strike to Harrison with 52 seconds left. But a leaping Harrison couldn't snag Schaefer's floater on the two-point conversion attempt.
Towson was held to minus-14 yards rushing in the first half, but its defense sacked Whitney five times. Bencivengo's 32-yard field goal with 5:19 remaining in the second quarter put the Tigers up 3-0.