Trailing 20-6 at half time, Cross (eight carries, 22 yards) scored on runs of 1 and 2 yards within 2 minutes of each other early in the third quarter, forging a 20-20 tie.
Taylor Martinez (12-for-20 passing, 171 yards) put Nebraska ahead for good in the fourth with a 5-yard TD toss to Jamal Turner and the Cornhuskers (8-2, 5-1 Big Ten) went on to win their fourth straight.
Martinez also ran the ball 15 times for 104 yards and Ameer Abdullah added 116 rushing yards on 31 carries.
Matthew McGloin led Penn State (6-4, 4-2), going 18-of-37 passing for 241 yards with a touchdown.
The Nittany Lions' Zach Zwinak paced all rushers with 141 yards and a TD on 21 carries.