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.
Graduate transfer quarterback Davis Webb has officially joined California, giving the Golden Bears an experienced option to replace No. 1 overall NFL draft pick Jared Goff.
First-year football coach Dino Babers, hired by former Syracuse AD Mark Coyle, is on the committee that will search for Coyle's replacement.
Hugh Freeze has some major holes to fill on offense with the departures of Laremy Tunsil and Laquon Treadwell, but there is Chady Kelly and good depth.
After transferring in from Montana State, Dakota Prukop has a checklist he's working from as he prepares to compete for the Oregon job.
The destination for Week 6 of the Big 12 Ultimate Road Trip is unanimous, as all three conference reporters would head to the Red River Rivalry.
The defense, as usual, looks solid at Missouri. But the offense will need to make rapid improvement under a new coaching staff.