Perry was originally recruited as a quarterback, but converted to slotback in the spring. Starting quarterback Zach Abey was active after suffering a shoulder injury last week against Temple, but Perry got the nod to run the triple-option offense and that proved to be a wise decision for Navy (6-3, 4-3 American Athletic Conference).
Perry had the third most rushing yards in school history before leaving late in the fourth quarter with an apparent leg injury.
SMU quarterback Ben Hicks threw a 29-yard touchdown to Courtland Sutton and then completed another pass to Trey Quinn for a 2-point conversion that tied the game, 40-40, with 3:32 remaining to play.
Garret Lewis entered for the injured Perry and handed the ball to fullback Anthony Gargiulo, who managed 50 yards on two carries to the Mustangs' 9-yard line that eventually set up the game-winning kick.
Gargiulo finished with a career-high 145 yards on 15 carries and had the game's first touchdown on a 4-yard run. The Midshipmen snapped a three-game losing streak and became bowl-eligible for the sixth consecutive season.
The Mustangs (6-4, 3-3) struggled against the Midshipmen's running attack, allowing 559 yards.
Perry gave Navy a 27-11 lead with a 92-yard touchdown scamper in the second quarter_the second longest run in school history.
Trailing 34-11 at the half, SMU got back in the game on a 14-yard touchdown pass from Hicks to Sutton and a 3-yard touchdown run by Xavier Jones early in the third quarter. Jones finished with 106 yards on 18 carries.