Adrian Diaz dunked, then converted a three-point play to give Florida International the lead, 39-37, but the Monarchs answered when Zoran Talley hit a jumper, Freeman drilled a 3-pointer and Brandan Stith dunked to put Old Dominion ahead, 44-39.
The Monarchs led by more than a field goal only once the rest of the way.
Freeman leads all Conference USA scorers with an average of 20.4 points per game, but his streak of five consecutive games with 28 or more points was snapped.
Aaron Bacote scored 15 points for Old Dominion (12-10, 5-4). Stith added 13 points and Denzell Taylor pulled down 11 rebounds.
Diaz scored 21 points to lead FIU (11-11, 5-4), with Daviyon Draper adding 19.