The Chippewas (4-4, 3-1 Mid-American) snapped a five-game skid against Ball State.
James Gilbert's 1-yard touchdown run on the final play of the first half gave Ball State (2-6, 1-3) its first lead of the game at 14-10.
Rush hit Jesse Kroll for a 4-yard score late in the third quarter and Brian Eavey made a career-long 47-yard field goal to put Central Michigan in front 20-14. But KeVonn Mabon returned the ensuing kickoff 89 yards for a touchdown and Ball State led 21-20 with 10:24 remaining.
The Chippewas answered with an 11-play, 55-yard drive, capped by Eavey's third field goal of the day - a 34-yarder - to take the lead for good.
Ball State, which has lost five in a row, turned it over on downs twice in the final 5:30.