TJ Malone and Ethan Long helped the Nittany Lions make up a once-six-point deficit.
Following their series downfall to the Cornhuskers, the Nittany Lions will not qualify for the Big Ten Tournament.
Historically, Princeton leads its series with Penn State 3-0, though the groups haven't faced each other since 1998.
The Nittany Lions struggled to contain Stony Brook's offensive firepower and were eliminated from the NCAA Tournament Friday night.
A strong defensive performance and efficiency on offense will be the keys to success over Stony Brook in the opening round of the NCAA Tournament.
A go-ahead Lexie Black home run was almost enough for the Nittany Lions, however, Indiana pulled off a walk-off victory in nine innings Thursday afternoon.