NCCU's Dante Holmes hit a 3-pointer with 32 seconds left in regulation that tied the game at 56-56.
Hilliard led the Eagles with a season-high 25 points. Jeremiah Ingram added a season-high 19 points and Jordan Parks scored 11 and grabbed 13 rebounds for his fifth double-double in his last six games.
The Eagles outshot the Tigers 48.7 to 34.8 percent while neither did well from the free-throw line, NCCU making 24 of 44 for 54.5 percent - but 7 of 9 in overtime - and the Tigers 28 of 42 for 66.7.
It was the third consecutive victory for the Eagles (9-5), who have won eight of their last 10.