The victory by the Aggies (15-15, 9-6 Mid-Eastern Athletic Conference) ended a three-year reign by the Bears (15-12, 10-5) as conference regular-season champions, giving Bethune-Cookman the No. 1 tournament seed.
North Carolina A&T led 46-34, in the second half, but after Morgan State cut it to six points, 60-54, Hill missed two free throws for the Aggies. A 3-pointer by the Bears' Aric Brooks made it 60-57 with 1:39 left.
Hill got three more chances to go to the line down the stretch and made both shots each time to keep the Aggies ahead.
Nic Simpson had 12 points and Hill 11 for the Aggies.