Villanova starting quarterback Antwon Young completed 16 of 26 passes for 172 yards and one touchdown, but also had four interceptions. Robert Irvin was 15-for-23 for 179 yards and a touchdown for the Quakers (0-1), who lost to the Wildcats for the seventh straight time since the series was resumed in 1999.
Penn led 14-7 on a 12-yard run by Michael DiMaggio with 9:56 left in the second quarter, but Villanova tied the score four plays later on a 38-yard pass play from Young to Matthew Szczur.
Neither team scored in the second half, although Villanova threatened on three occasions but was stopped by Penn's interceptions.
Whitney replaced Young late in the game and completed 1 of 2 passes for 10 yards and carried four times for 25 yards and a touchdown.
Villanova now has an 8-5 lead in the overall series, which started in 1905 - but the teams didn't play from 1912 to 1999.