Ball State had a chance to tie at the end of regulation, but Scott Secor's 38-yard field goal attempt was blocked as time expired.
Arkansas State (8-5) won the GoDaddy Bowl for a second straight season, despite losing starting quarterback Adam Kennedy to a knee injury in the second quarter. It was the Red Wolves' third straight trip to Mobile.
Knighten had 115 yards passing and 97 yards rushing.
Ball State (10-3) pushed ahead 20-16 with 1:33 remaining on a 1-yard touchdown run by Jahwan Edwards, but couldn't hold the lead. Edwards finished with a game-high 146 yards rushing.
Keith Wenning capped his Ball State career with 215 yards passing, one touchdown and one interception.
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