Jacson McGowan and Skyler Hunter also drove in a pair of runs for the second-seeded Boilermakers (38-20), who lost to Houston on Friday. Purdue trailed 3-2 after three innings but scored four runs in the fourth then added six in the sixth to take control.
Trent Johnson (3-1) took the win with a scoreless inning of work.
Forest Kimbrell, Dawnoven Smith and Greg White drove in runs for the fourth-seeded Aggies (32-25), the Mid-Eastern Athletic Conference champions who lost to regional host and No. 6 national seed North Carolina on Friday.
Michael Johnson (7-2) took the loss, allowing six runs and 10 hits in 3 2/3 innings.
The game stopped in the eighth for a 2½-hour rain and lightning delay.
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