With the win Harvard clinched at least a share of its 16th Ivy League title and eighth under head coach Tim Murphy.
Harvard (9-0, 6-0 Ivy) had to struggle to put away Penn (1-8, 1-5) as the Quakers led 24-17 with 6:34 remaining in the third quarter.
Andrew Flesher kicked a 38-yard field goal in the fourth to close to 24-20. On the next series Scott Hosch hit Tyler Hamblin on a 28-yard scoring strike to retake the lead. Stanton rushed in for a score from the 14 with 6:42 remaining to seal the win.
Stanton also had touchdown runs of 42 yards on the Crimson's first play and a 75-yarder in the second quarter.
Alex Torgersen led the Quakers, throwing for 211 yards and one touchdown.