Receiver Rodney Adams caught five balls for a career-high 118 yards and three touchdowns as the Bulls (3-3, 1-1 American) put together back-to-back wins for the first time since October 2013.
Marlon Mack rushed for 113 yards, all but nine of those coming in the second half. His 59-yard run down the left sideline in the third quarter set up a 15-yard touchdown scramble by Flowers that gave the Bulls a 21-13 lead.
Quarterback Bryant Shirreffs completed 28 of 41 passes for 365 yards and a touchdown for UConn (3-4, 1-2). He also ran for 100 yards, but was sacked five times.
Running back Arkeel Newsome added 221 all-purpose yards for the Huskies.