The Orange (7-5, 5-2 Big East) have won five of six games to finish the season, and now await their bowl destination. Syracuse is moving to the ACC next season.
Temple took a 20-17 lead midway through the third quarter on quarterback Clinton Granger's 10-yard scamper that capped a four-play, 62-yard Owls drive.
But the Orange took over from there.
Syracuse marched down the field on its ensuing possession, going 75 yards on 12 plays over 4:21 and ending it with Aimeen-Moore's 1-yard plunge to take a 24-20 lead with 4:37 left in the quarter.
Prince-Tyson Gulley scored on a 3-yard run early in the fourth quarter, ending an 11-play, 75-yard drive that took up 4:04 and gave them a 31-20 advantage.
Syracuse clinched it on Keon Lyn's 31-yard interception return of Granger's errant pass with 2:37 left in the game. It was the first of two interceptions for Lyn.
Temple's Montel Harris, who ran for 351 yards and seven touchdowns in last Saturday's record-setting, 63-32 win over Army, ran for 106 yards on 21 carries for the Owls (4-7, 2-5), who ended their first season back in the Big East by losing five of six.