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 with just over 3 minutes left in the half. The Owls were driving again before Harris was stripped of the ball by linebacker Yawin Smallwood at Connecticut's 26-yard line with 19 seconds before intermission.
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.
The Huskies came in ranked sixth in the nation in total defense, giving up just over 82 yards per game on the ground. But Temple ran for 202. Harris, who transferred from Boston College, had his second consecutive 100-yard day, after gaining 133 yards in the Owls' win last week over South Florida.
The win gave Temple coach Steve 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
The win gave Temple its first road win of the season.
Temple improved to 9-4 against UConn and has won two in a row.