Nova's mistakes kept Navy (2-4) in the game until the final snap, but he made two key throws to lead the comeback and the defense and special teams took care of the rest.
"That was a buzz saw we ran into today and our back was against the wall," said head coach Greg Schiano. "Those are our nation's elite as far as fighting. I'm really proud of our guys because at no point did they panic."
The true freshman, in his second career start, threw second-half touchdown passes to Quron Pratt and Tim Wright. At the start of the fourth quarter, Nova snuck a pass between two defenders to Wright in the back of the end zone to take the lead.
Like the Syracuse comeback, Nova managed the game, but made mistakes to keep the opponent in contention.
Like the Syracuse comeback, defense and special teams won the game in the end.
"I have to learn from this experience," Nova said. "Stop being careless with the ball, make smart decisions."
"We thought we had an opportunity there," Schiano said. "... I thought Brandon Jones did it exactly as it was called, extended his body, sacrificed his body."
Nova remains unbeaten in games where he took a snap at quarterback, continuing a streak dating back to eighth grade, but made multiple costly mistakes.
Nova's biggest mistake came when he forced a ball to Paul Carrezola that went for six the other way on an interception.
The second interception came deep in Rutgers territory in the fourth quarter. With Rutgers leading by a point, Nova threw an interception that placed Navy on the 28-yard line.
But yet again, the rewards outweighed the risks for Nova, who finished with 271 yards, two touchdowns and completed 23 of 31 passes.
"That's an NFL throw," Schiano said of the Wright touchdown. "You're going to live with some growing pains, but not at all cost. We have another good quarterback on the roster (Chas Dodd) and Frank [Cignetti] and I talk about it all the time."
Running back Jawan Jamison had his best performance of the season. Jamison exceeded 100 yards and ran for his first career touchdown on 22 attempts.
Fullback Joe Martinek moved the chains, averaging 12.3 yards per touch. Wide receiver Mohamed Sanu, yet again, did what he does best. Sanu caught the ball 10 times for 100 yards. He remains the top receiving target.
Navy's triple option disrupted Rutgers' defensive rhythm initially, but the defense adjusted and held the Midshipmen to 162 rushing yards.
Quarterback Kriss Proctor broke a 54-yard touchdown run and caught a 37-yard pass. Other than those two big plays, the defense shut down the triple option.
"I thought they battled to the end," said Navy head coach Ken Niumatalolo. "Unfortunately, we had some mistakes, some similar things that have happened in the past, that we couldn't find a way to finish it. I liked the effort. I thought our guys battled. That is a good football team."
Rutgers (5-1, 2-0) is within one game of bowl eligibility and gets its chance Friday night in Louisville.