Joe Miller went four innings on the mound for the Quakers, surrendering four runs on five hits.
The Aggies scored three runs in the first inning and two more in the fifth to account for their offensive output in Game 1.
Penn battled back in Game 2, relying on a five-run ninth to beat the Aggies and win the series.
Craig Larsen drilled a three-run double to right field to highlight the final frame, while Wyatt Henseler followed with a double to score Larsen.
Henseler finished the contest 4-for-4 with three RBIs.