Villanova had a six-run lead at one point, but The Citadel put together a six-run eighth inning to defeat the Wildcats in their series finale on Sunday, 13-10.
Jack O'Reilly led the Wildcats with two hits, while Joey Castellanos collected two RBIs.
Cameron Hassert plated two with an RBI double in the top of the ninth.
Devin Rivera threw 72 pitches for the Wildcats but lasted just 2 2/3 innings, surrendering two runs on four hits.
Cole Vanderslice took the loss, surrendering four runs while collecting only two outs. He walked a pair and gave up two hits. The Wildcats staff combined on the day to issue 15 walks.
Chris Rotondo finished 1-for-3 for Villanova with a pair of walks and three runs scored.
The Wildcats (1-5) will be back in action on Wednesday with a contest against Charleston Southern.