The victory kept Western Kentucky from going winless in nonconference games to start the season.
Duncan came on in the second half and gave Western Kentucky an immediate lift as the Hilltoppers drove for a touchdown to take a 14-13 lead on a 4-yard pass to Mik'Quan Deane with 2:53 left in the third quarter.
Riley Neal found Corey Lacanaria with a 6-yard touchdown pass to put the Cardinals up, 20-14 with 8:39 to play, but Duncan engineered two scores in the final five minutes to earn the win.
Duncan hit Deane from 18-yards out to put WKU (1-3) in front, 21-20, then engineered an eight-play, 70-yard drive capped by Joshua Samuel's five-yard run with :59 left.
Neal hit Riley Miller with a 34-yard pass to give Ball State (1-3) a first down at the Western Kentucky 48, and a pass interference penalty put the Cardinals at the Hilltoppers' 33, but DeAndre Farris and Spencer Gaddis broke up Neal passes to seal the victory.
