Wagner (3-10, 1-1 Northeast Conference) was down by as many as 15 in the second half, but stormed back as Burton scored nine points during a 16-3 run to tie the game at 60.
Wagner took its first lead of the second half with 1:35 left. Mount St. Joseph scored the next four for a 67-64 advantage, but Burton stole the ball with 12 seconds left and found Romone Saunders for a 3-pointer.
Junior Robinson made consecutive baskets to give Mount St. Mary's (4-9, 0-2) a 78-76 lead in overtime, but Burton sent the game to double overtime.
Saunders scored three of his 15 points to start the second overtime, Mount St. Mary's didn't make a field goal in the final five minutes and Burton made the game-winning free throws.