Ball, who finished with 20 carries, helped the Wildcats (1-1) rush for 330 yards. Matt Szczur ran for 95 yards and Angelo Babbaro added 68 yards rushing and an 8-yard touchdown run in the second quarter.
Whitney completed 8 of 13 passes for 129 yards and two interceptions. He had touchdown throws of 39 yards to Dorian Wells and a 7-yard passing score to Chris Farmer to give Villanova a 28-0 lead in the third quarter.
Wells had three catches for 99 yards for the Wildcats.
The Mountain Hawks (1-1) were shut out for the first time since Oct. 17, 2009 -- a 7-0 home loss against Yale.
Chris Lum went 18-for-31 passing for 172 yards and threw three interceptions.