Trailing by six points with 15:09 to play, Freeman scored eight points during a 16-3 run to give Old Dominion a 49-41 lead with 10:14 left, and the Monarchs led the rest of the way.
Freeman shot 11 of 16 from the floor. Richard Ross scored 11 points and Aaron Bacote chipped in 10 for Old Dominion (17-4, 6-3 Conference USA). Jonathan Arledge added nine points with six rebounds and four assists.
Solomon Poole scored 15 points and Kelvin Penn grabbed 12 boards to lead Florida Atlantic (8-10, 1-6). Justin Massey scored 11 points and Marquan Botley added 10 for the Owls, who shot 18 of 48 (37.5 percent) from the field.