Four late free throw conversions by Malik Smith in the final 30 seconds and one by Elliott Eliason with 33 seconds, enabled the Gophers (13-3, 2-1 Big Ten) to hang on after taking its first lead of the second half with 1:43 remaining.
Tim Frazier scored 20 points for Penn State (9-7, 0-3) but was unable to finish the game after injuring his right leg with 2:08 left and Penn State leading 59-57.
Mathieu forced back-to-back Penn State turnovers, including a strip of John Johnson and his ensuing basket gave the Gophers a 63-60 lead and forced Penn State to foul.
The Nittany Lions' Allen Roberts missed a game-tying 3-point shot with 1 second to go.
Minnesota, which has won 30 out of 40 games in its series with Penn State, also got 11 points and 12 rebounds from Eliason.
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