Morgan State led 28-21 in the third quarter after three Robert Counsel touchdown passes, including a 75-yarder to Thomas Martin.
Eastern Michigan responded with a 10-play, 76-yard drive, culminating with Ryan Brumfield's 14-yard scoring run. After holding the Bears to a three-and-out at the end of the third, Eastern went nine plays and 45 yards to set up the game-winner.
Morgan State scored first as Lamont Brown III capped a 13-play, 75-yard drive with a 3-yard touchdown run.
The Eagles then scored three straight touchdowns. Darius Jackson plunged from the 1, Emu Adams recovered a blocked punt to score and Brumfield had a 16-yard run.
The game was delayed late in the fourth quarter due to weather conditions.