The Huskies drove 42 yards downfield in 3 minutes, 40 seconds to the Missouri 25-yard line to set up a 42-yard field goal.
As Bobby Puyol lined up to take the kick, holder Tim Boyle faked a handoff and lined up to throw, but his pass down the middle of the field was intercepted by Anthony Sherrils to seal the win for Missouri (3-0).
Missouri took its first lead of the game on Maty Mauk's two-yard touchdown run on fourth-and-goal with 5:03 left in the third quarter.
Quarterback Bryant Shirreffs threw for 156 yards and ran for 29 yards on 14 attempts for the Huskies (2-1). Ron Johnson had 14 carries for 23 yards and a touchdown.
The Huskies, who committed eight penalties for 85 yards, got off to a slow start when a punt was blocked out of the end zone for a safety, as Missouri took a 2-0 lead.
UConn scored on Johnson's touchdown with 4:14 left in the first quarter but Puyol's PAT was blocked.
Michael Tarbutt missed a 49-yard field goal on UConn's first drive of the second half. UConn went 2-for-13 on third down.
UConn opens American Athletic Conference play against Navy on Sept. 26.