Penn State's pitching was instrumental by only allowing Northwestern to score two runs.
The Nittany Lions have now lost to the Trojans twice this season.
The Nittany Lions season ended one game after taking a third straight conference title.
The Nittany Lions found it difficult to find their footing in the second half despite their strong start.
Paxton Kling led the way for Penn State's bats with five hits.
Six Nittany Lions had at least three points in the victory.