Jawan Jamison scored on a 1-yard touchdown run, Gary Nova threw a 12-yard touchdown to Tyler Kroft and walk-on placekicker Nick Borgese had a 25-yard field goal filling in for the injured Kyle Federico as the Scarlet Knights went 6-0 for only the third time since 1976.
The Orange had the blocked field goal when they were poised to take the lead, four turnovers, untimely penalties and failures in Rutgers' territory.
With Syracuse headed to the ACC next season, this was the final conference game between the schools, and it was one the Orange were in position to win. They tied the score just before halftime with an 80-yard drive and had another drive going after taking the second-half kickoff and moving to Rutgers 15.
Ross Krautman, who kicked a game-winning field goal here two years ago and came into the game as the conference's active leader in field goal percentage, lined up for a 32-yard attempt. Linebacker Jamal Merrell broke through and got a hand on the kick, which rolled toward the Syracuse bench. Harmon collected it, got a convoy of blockers, and scored for a 14-7 lead.
The blocked kick was the 27th for Rutgers since 2009, best in the nation among major schools.
Jamison, who had his streak of six straight 100-yard games rushing snapped at six with 64 yards on 28 carries, ran seven times on the ensuing drive and Nova hit Brandon Coleman for 16 yards to set up Borgese's kick. He played because Federico was hurt last week against Connecticut.
Greene, who had 14 tackles in the game, forced Steve Rene to fumble on a punt return on the first play of the fourth quarter and Kevin Snyder recovered. Nova hit Kroft on third down for a touchdown. Borgese missed the extra points and it almost hurt the Scarlet Knights.
Nassib (25-of 42 for 356 yards) got the Orange within eight points with less than five minutes to play and Syracuse got the ball back with 2:45 to play. However, Brandon Jones intercepted Nassib on first down and Rutgers ran out the clock.
Jamison gave Rutgers a 7-0 lead with his short touchdown run, which capped a season-long 93-yard drive. Nova (14 of 23 for 152) set up the score with a 43-yard pass to Coleman to the 1-yard line.
Syracuse converted three third-down plays in its 80-yard drive that ended with Ameen-Moore powering into the end zone against the nation's No. 2 ranked run defense.