Thomas opened the scoring with a 4-yard run in the first quarter before Owens found Morgan Williams, Bernard Reedy, Cassius McDowell and Eric Page for scores. Owens finished with 267 yards passing, 145 of them to Page, for the Rockets (8-4, 7-1 Mid-American).
Jahwan Edwards and Dwayne Donnigan added rushing touchdowns for Ball State.
Despite the win, Toledo missed out on a MAC Championship Game berth when Northern Illinois beat Eastern Michigan. The Rockets will likely play in the Little Caesars Pizza Bowl Dec. 27 in Detroit.