Nearly 6,000 fans attended the extra-innings thriller in downtown Indianapolis.
It was a game of almosts for the Cardinals (21-20, 8-7 MAC), who haven't beaten the Hoosiers (22-16-2, 8-6-1 Big Ten) since April 17, 2013.
The Bulls are shutting down their baseball program after this season.
The Cardinals are hitting .401 in their last seven games after hitting .207 during their nine-game losing streak.
Ball State baseball (18-18, 6-6 MAC) scored 36 combined runs in Saturday's doubleheader to sweep Bowling Green (9-22, 4-8 MAC).