"Jazz this is for you," coach Randy Edsall said, referring to Howard by his nickname. "Best win we have ever had."
The loss was the third straight for Notre Dame (6-5) and will add to the mounting calls for Weis to be fired. The Irish led 14-0 early in the second quarter but didn't score another touchdown until the first overtime.
The Huskies (5-5) had lost three straight painfully close games since Howard was killed. This time they made the plays at the end to win in dramatic fashion.
Jordan Todman ran for 130 yards on 26 carries, including a 43-yard TD run for UConn. He also added a 96-yard kickoff return for a TD. Dixon rushed for 114 yards on 20 carries.
Notre Dame was upset last season by Syracuse in its final home game of the season.
Jimmy Clausen was 30 of 45 passing for 329 yards for Notre Dame. Golden Tate had nine catches for 123 yards and Michael Floyd had eight catches for 104 yards.