Aune hit Shorter for a 25-yard touchdown to open the scoring. Aune sandwiched touchdown throws to Shorter covering 2 and 25 yards around a pick-6 by Ridge Texada and North Texas (3-3, 2-0 Conference USA) led 28-7 with 5:36 left in the second quarter.
Florida Atlantic (2-4, 1-1) got within seven points at halftime after Teja Young picked off an Aune pass and returned it 64 yards for a touchdown. N'Kosi Perry threw a 35-yard scoring strike to Larry McCammon with 21 seconds left before intermission.
Aune completed 14 of 20 passes for 180 yards. Ragsdale carried 16 times for 119 yards.
Perry completed 26 of 50 passes for 295 yards and two touchdowns with two interceptions for FAU. LaJohntay Wester had 10 catches for 113 yards and a score.
North Texas finished with 300 yards on the ground, rushing 51 times.