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.
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.
The Nittany Lions cruised behind a six-run sixth inning.
Colin Fitzgerald struck out a career-high 12, but the Nittany Lions fell short of a season-defining upset victory.