Marcus Burton hit three free throws with 1:06 left in overtime, giving Wagner an 81-78 lead.
Gloger grabbed an offensive rebound of a missed 3 by Valjarevic and Calixte made a layup to pull the Black Bears within one with 33 seconds left.
Valjarevic fouled and Greg Senat missed the front end of a one-and-one 14 seconds later.
Valjarevic missed a jumper with 4 seconds to go, but the ball went out of bounds off of Wagner (2-4), setting up the winner as time expired.
Burton scored a career-high 25 to lead Wagner. Mike Aaman added 15 points and 11 rebounds.