Wilbert, who then completed a two-point conversion pass, drove the Owls (2-6, 1-4 Sun Belt Conference) 74 yards in nine plays after the Trojans (4-4, 3-3) went ahead 27-26 on Shawn Southward's 31-yard run with 1:49 remaining.
The victory ended a six-game skid for the Owls, who lost 37-34 in double overtime to South Alabama last week. It also ended their streak of 14 conference losses, dating to 2010.
FAU led 17-0, but Troy tied it after scoring two touchdowns in the final two minutes of the first half. The second was set up by an Owls fumble at their 29.
Mitch Anderson's 47-yard field goal broke the tie and Wilbert's third touchdown pass made it 26-17 with 3:49 left in the third quarter.
Soon after ESPN 300 quarterback Tate Martell of Las Vegas Bishop Gorman decommitted from Texas A&M via Twitter, Aggies receivers coach Aaron Moorehead tweeted about "loyalty."
UCLA athletic director Dan Guerrero says he's ready to move on from episode in which his decision to vote incorrectly as a Pac-12 rep led to a public admonishment from the commissioner.
SEC Network's Paul Finebaum reacts to the Ole Miss uproar after ESPN's KC Joyner predicted the Rebels will go 7-5 in 2016.
AP's Ralph Russo joins The Paul Finebaum Show to break down what could happen if the Big 12 extends its conference.
Hall of Fame RB Eric Dickerson joins Highly Questionable to share the craziest offers he received while being recruited by colleges, as well as recounts why he decommitted from Oklahoma to go to SMU.
With so many departures and holes to fill across the division, no team is in great shape at linebacker.