"Overall, I think we played pretty well; we've just got to be able to finish," Whitmer said.
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. Temple ran for 202.
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.
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.
Pasqualoni was the head coach at Western Connecticut and hired Addazio to his first assistant coaching job there in 1985.