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.
Florida State coach Jimbo Fisher hopes quarterback Sean Maguire is ready to go full speed by the middle of June.
Graduate transfer quarterback Davis Webb has officially joined California, giving the Golden Bears an experienced option to replace No. 1 overall NFL draft pick Jared Goff.
First-year football coach Dino Babers, hired by former Syracuse AD Mark Coyle, is on the committee that will search for Coyle's replacement.
Hugh Freeze has some major holes to fill on offense with the departures of Laremy Tunsil and Laquon Treadwell, but there is Chady Kelly and good depth.
After transferring in from Montana State, Dakota Prukop has a checklist he's working from as he prepares to compete for the Oregon job.
The destination for Week 6 of the Big 12 Ultimate Road Trip is unanimous, as all three conference reporters would head to the Red River Rivalry.