Head coach Mike Gambino was ejected in the sixth inning.
Penn State closed out the series by scoring 10 runs.
The Nittany Lions will play UC Irvine in the first round of Mark Pavlik's final appearance in the NCAA Tournament.
Penn State wrestling put together a strong showing at the U.S. Open, highlighted by multiple podium finishes.
For the second night in a row, Penn State led the No. 19 Ducks in the seventh and couldn't finish them off.
The Nittany Lions win their fourth consecutive EIVA Tournament title in Mark Pavlik's final home match.