Jalen Fitzpatrick caught a 14 yard touchdown pass with 19 seconds left in regulation, and Brandon McManus kicked a 29-yard field goal in overtime to give the Owls a 17-14 victory and back-to-back Big East wins for the first time in program history.
"This team's got that fight in 'em; they've got that will in 'em; they've got that stuff that is the great foundation of a building of a program," said coach Steve Addazio.
Boston College transfer Montel Harris ran 30 times for 142 yards and a touchdown for the Owls (3-2, 2-0 Big East), who held UConn (3-4, 0-2) to two first-quarter touchdowns.
"Our defense is tough, we're really tough, said freshman linebacker Tyler Matakavich, who is from nearby Stratford and led Temple with 19 tackles. "We're going to battle till the end of the game."
The Huskies' Chad Christen missed four field goal attempts, including a 28-yarder on UConn's overtime possession.
"Field goals aren't automatic," Christen said. "I did my best and missed it."
Chandler Whitmer threw for 293 yards and both of UConn's scores, and Max DeLorenzo had 91 yards rushing for the Huskies.
Temple trailed until Jalen Fitzpatrick caught a 14-yard touchdown pass from Chris Coyer with 19 seconds in regulation. Fitzpatrick said he tried to sell another route, then went to the right on a corner pattern and found himself open.
The touchdown was set up by a 33-yard catch on the left sideline by Deon Miller on a third-and-13 from the UConn 47, which followed 13-yard catch by Harris on a fourth down that moved the ball into UConn territory.
Temple had failed on fourth down on two other fourth-quarter drives.
"They did a good job containing our throw game," said Fitzpatrick. "But on the last drive you saw a couple of great plays made."
Christen had a chance to secure the win for UConn, but his 45-yard field-goal attempt with just under 3 minutes to play was blocked by Miller. He had missed earlier from 38 and 42 yards.
Whitmer completed 10 of his first 12 passes, including a 15-yard strike over the middle to Mike Smith for a touchdown that gave the Huskies a 7-0 lead. On his next drive, he found tight end Ryan Griffin over the middle for a 42-yard score.
Whitmer completed 22 of 39 passes with no interceptions. He had thrown four interceptions in a loss to Rutgers last week and came in with 10 on the season and just four touchdown passes.
Coyer, who threw for just 132 yards, also ran for 51 for the Owls.
The Huskies came in ranked sixth in the nation in total defense, giving up just over 82 yards per game on the ground.
Both teams played without their top running backs. Temple's Matt Brown suffered an ankle injury last week, and UConn's Lyle McCombs sprained his wrist.
Without McCombs, the Huskies managed just 88 rushing yards. Temple ran for 202.
Harris, who transferred from Boston College, had his second consecutive 100-yard day coming off a hamstring injury. He had 133 yards in the Owls' win last week over South Florida,
"Coming back, being able to fight through adversity and being able to be the same person I am, that's just a great accomplishment and I look forward to getting better every week," he said.
The Huskies kept Temple pinned in its own territory for most of the first half. The Owls managed just 8 yards and one first down on their first four possessions. But they had 113 on their next two.
Harris broke a 37-yard run and a 24-yarder for a touchdown to cut the deficit to 14-7. The Owls were driving again before Harris was stripped of the ball by linebacker Yawin Smallwood at Connecticut's 26-yard line just 19 seconds before intermission.
The win gave Addazio a victory over his mentor.
UConn's Paul Pasqualoni was the head coach at Western Connecticut and hired Addazio to his first assistant coaching job there in 1985.
"I think what's really terrific is that we're getting out of here 2-0 in the Big East conference, 3-2 overall, with a young team,'" he said. "So the future is bright."