Javoris Bryant added nine points and 11 rebounds for the Wildcats (6-11, 1-1), who won the rebounding battle 42-33.
Lamont Middleton paced the Aggies (7-10, 0-2) with 25 points, including a 9 of 10 performance at the foul line.
Bethune-Cookman trailed 35-31 with 2:48 left in the first half but closed out the period with a 3 from Jackson and a layup and 3-pointer from Dukes for a 39-35 lead.
The Aggies came back and led 47-43 with 13:39 left. The lead changed hands five times from there, and the teams were tied 56-all with 5:55 left when Dukes hit a 3-point shot and added two free throws after a technical foul by North Carolina A&T. Dukes' 3-pointer sparked a 16-1 Wildcat run for a 72-57 advantage.