Clark completed 22-of-31 passes for 274 yards with a 53-yard fourth-quarter touchdown pass to Derek Moye.
He added a 2-yard second-quarter touchdown run.
Royster gained 118 yards on 15 carries, scoring on a 69-yard fourth-quarter run.
Moye finished with six receptions for 123 yards.
Collin Wagner kicked two field goals, and Brandon Beachum had one touchdown for the Nittany Lions (8-1, 4-1), who overcame a 10-3 second-quarter deficit to win their fifth in a row.
Northwestern quarterbacks Mike Kafka and Dan Persa combined for 243 passing yards.
Kafka scored on a 7-yard second-quarter run, while Stefan Demos kicked two field goals for the Wildcats (5-4, 2-3), who were out-gained 437-371 in total yards.