Three of Gradkowski's scoring throws went to Lance Moore as the Rockets won the MAC title for the second time in four seasons.
Gradkowski completed 18 of 24 passes for 251 yards and Scooter McDougle added 167 yards on 35 carries. Toledo, which will play Connecticut in the Motor City Bowl on Dec. 27, climbed to 9-3 and was 8-1 against MAC opponents.
Miami's Josh Betts was 20 of 33 for 304 yards with three touchdowns and two interceptions. Miami had a seven-game winning streak snapped and dropped to 8-4 and 7-2.
Miami was the winner of last year's conference championship game with current Pittsburgh star Ben Roethlisberger as its quarterback.