Kalu Ezikpe's fast-break dunk with nine seconds remaining sealed it for the Monarchs.
A.J. Oliver II had 12 points for Old Dominion (7-12, 3-3 Conference USA). Malik Curry added 11 points, and Aaron Carver had seven points and 15 rebounds.
Drew Edwards had 18 points for the 49ers (10-7, 4-2). Jordan Shepherd added 15 points and six assists, and Jahmir Young had 11 points and six rebounds.
The Monarchs evened the season series against the 49ers with the win. Charlotte defeated Old Dominion 53-47 on Jan. 11. Old Dominion faces Florida International at home on Thursday. Charlotte matches up against Florida Atlantic at home on Thursday.
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