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.
Joey Counts scored on a 1-yard run on fourth-and-goal with 2 seconds left to give Montana a 38-35 victory over four-time defending FCS champion North Dakota State on Saturday.
Transfer Vernon Adams will be the starting quarterback when Oregon begins its season against Eastern Washington on Sept. 5.
Tim Beckman is threatening legal action after Illinois fired him as football coach Friday amid allegations of influencing medical decisions and pressuring players to play hurt.
LSU offensive coordinator Cam Cameron revealed in a post-practice news conference that he has been treated for prostate cancer but plans to coach this season.
The woman who accused former Baylor defensive end Sam Ukwuachu of raping her in 2013 has hired a Title IX law firm to represent her in potential civil litigation.
Arkansas tight end C.J. O'Grady has been arrested by Fayetteville police and charged with driving while intoxicated and being a minor in possession of alcohol.