Tony Johnson scored four points in the second overtime, helping Lafayette back from a 70-64 deficit. Johnson found Mower for the game-winning basket after taking the inbounds with less than 7 seconds to play.
The Leopards (13-18), who lost to Lehigh in last year's final, had to force both overtimes.
Ryan Willen hit a 3-pointer with 13 seconds left in regulation to tie it at 53, and Mower hit 1 of 2 free throws with 12 seconds left in the first OT to tie it at 62.
Vlad Moldoveanu scored six of his 25 points for the Eagles (22-9) in the second OT, including a jumper that made it 70-64.
But Jared Mintz, who finished with 18 points, hit a jumper and a pair of foul shots to help key a 6-0 run that tied it at 70.