Stewart was 18-of-23 passing for 222 yards and threw all three of his scores to Brad Rozner, who finished with eight catches for 130 yards. Walter had 15 carries that included a 34-yard touchdown run.
Stewart threw TD passes from the 30 and 18, and his 34-yarder with 14 seconds left in the second quarter gave the Owls (1-9, 1-5 Conference USA) a 31-14 halftime lead.
Asher O'Hara threw for 338 yards and two touchdown passes and ran for another score for Middle Tennessee (3-7, 2-4).
The Blue Raiders fumbled the ball away on their first play from scrimmage but made it close with O'Hara's 7-yard touchdown run in the third quarter, and O'Hara's 20-yard touchdown pass to Jimmy Marshall with 3:22 remaining.
On the final drive, Rice converted on third-and-11 and chewed up more than three minutes of clock before punting into the Middle Tennessee end zone with 16 seconds remaining.
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