Riley Neal, a sophomore quarterback, pulled the game out for Ball State with a two-yard touchdown run with 1:47 remaining. Neal ran for two touchdowns and threw for two others in a 31-27 victory.
Jason Driskel threw for 324 yards for FAU, but his fourth-and-15 pass in the final minute was intercepted.
The Owls led 27-24 and tried to close out the game with 7:48 to play, but Greg Howell was stopped for no gain.
FAU, 1-3, took a 14-0 first quarter lead and 24-17 at the half. The game was delayed four times because of lightning.
Kalib Woods caught passes for 108 yards for FAU for the game.
Neal threw for 252 yards and ran for 74 to lead Ball State, 3-1.
FAU opens its Conference USA schedule with a trip to FIU.