Gillett ran for 189 yards and two TDs and threw for 225 yards and three scores as the Eagles (1-6, 1/3 Mid-American Conference) won their first game since Nov. 28, 2008.
Ball State took a 38-35 lead on Ian McGarvey's field goal on the first possession of OT before Thayer scored his second TD of the game.
Eastern Michigan trailed 28-7 late in the second quarter but rallied with 28 unanswered points.
Ball State then tied it at 35-all when Wenning hit Briggs Orsbon with a 9-yard TD pass with 34 seconds left in regulation.
Jim Harbaugh participated Tuesday in an annual walk to the graves of Bo Schembechler and Fielding Yost, and the current Wolverines coach smashed a buckeye at the grave of his former coach.
In a push for bowl eligibility, the University of California has asked the NCAA to allow its season-opening win over FCS school Grambling State to count toward the necessary six wins.
Michigan football coach Jim Harbaugh smashes a buckeye at former Michigan football coach Bo Schembechler's grave. Harbaugh's father and Michigan fans joined in to honor Schembechler. Michigan plays the rival Ohio State Buckeyes on Saturday.
The 3-point stance discusses the late-season issues the nation's top receivers are having, the fitting Hornung Award finalists, and Oklahoma State.
Tennessee coach Butch Jones and Vanderbilt coach Derek Mason discuss their preparations for Week 13.
SEC Network's Greg McElroy and Jabari Greer discuss how Georgia will be able to contain Georgia Tech's offense.