MarQueis Gray, the Gophers' starting quarterback, simply couldn't play because of an injured toe on his left foot.
''We did everything we could to get MarQueis ready to play, but he just wasn't ready,'' Kill said. ''You can't play on one leg.''
Shortell was 11 of 22 for 104 yards and led a unit that went 0 for 11 on third-down conversions.
''Our defense was on the field almost all of the first half,'' Shortell said. ''So we couldn't run a lot of plays because we didn't have the ball.''
Kill was on the sideline just days after leaving the team seeking more treatment for seizures he's had the past three weeks and dismissed the thought that his health was a distraction.
''I only missed one practice,'' Kill said. ''I've never missed a game in my life. You can't use that as an excuse.''
Kill credited Michigan's defense with making Shortell's debut as a starter a rough one.
''They put a lot of pressure on him,'' Kill said. ''When you have a rookie quarterback, you're going to get a lot of guys in his face.''
Minnesota (1-4, 1-0 Big Ten) trailed Michigan (5-0, 1-0) by more than five touchdowns in the first half and gave up 20 more points after halftime.
The Wolverines had their most lopsided win since beating Indiana by the same score in 2000.
Denard Robinson threw two touchdown passes and ran for a TD. Vincent Smith scored on a run, pass and catch to help Michigan lead 38-0 at halftime.
The Wolverines outgained Minnesota 384-69 in the first half, averaging nearly 10 yards per play. Nothing went well for Minnesota all day.
The Gophers got into Wolverines' territory only once before halftime and fumbled on the play.
They stopped Michigan on its first drive of the second half and got to midfield on the punt return, but spoiled the play with a penalty. Minnesota dropped a pass past the 50 on its next possession and had a 96-yard kickoff return wiped out by another flag.
Minnesota didn't take a snap in Michigan territory until there was less than a minute left in the third quarter.
And just when it looked as if the Gophers were going to score, David Cobb fumbled and cornerback Courtney Avery scooped it up on an 83-yard return for a 58-0 lead with 4:58 left.
The Wolverines kept the Little Brown Jug trophy that the teams have played for since 1909.