Penn (3-0) ended a four-game losing streak against Dartmouth (1-2, 0-1) and is off to its best start since since 2003.
Aidan Sayin threw a 5-yard touchdown pass to Joshua Casilli in the first overtime that gave Penn a 17-10 lead. Dartmouth answered with quarterback Nick Howard's 5-yard touchdown run.
Penn blocked Dartmouth's field goal attempt in the second OT before Flower's game-winning run.
Graham Gotlieb kicked a 35-yard field goal for Penn as time expired in regulation to force overtime tied at 10.
It was Penn's first double-overtime game since 2013.
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