Penn took a 27-17 lead early in the fourth quarter when Luke DeLuca scored on a 1-yard run. DeLuca's run came one play after Brad Blackmon rushed for 55 yards on third-and-2.
Andrew Samson then kicked a 29-yard field goal with 1:09 left to play. Samson finished with three field goals, including kicks of 39 and 35 yards.
The Quakers opened the scoring on a Jim McGoldrick blocked punt of Matthew Kelly in the end zone for a 7-0 lead with 12:50 left in the first quarter.
Alex Jenny was 23-for-38 with 204 yards, two touchdowns and one interception for the Big Green (0-3, 0-1).