Wiggins took over what had been a tight contest in the home stretch, scoring 15 of the game's final 19 points to give Kansas (2-0) the win in the second game of the Champions Classic in Chicago.
Second-ranked Michigan State topped Kentucky in Tuesday's opening game.
Ellis had seven rebounds and hit 5-of-6 free throws. The Jayhawks were a solid 27-of-35 from the foul line Tuesday.
Amile Jefferson scored 17 to lead Duke (1-1). Rasheed Sulaimon scored 13 and Rodney added 11.
Duke led 42-40 at halftime but Kansas, which shot 56.1 percent from the field, took an 87-81 lead with 1:17 to play and snapped off seven free throws down the stretch to keep Duke at bay.