A 64-yard scoring burst from Whatley following an FAU turnover gave Middle Tennessee a 35-28 lead with 1:32 remaining. But Johnson found Lucky Whitehead for a 21-yard touchdown on fourth down with three seconds remaining to send the game into overtime.
Middle Tennessee's Jordan Parker added 115 yards rushing and a score, eclipsing the 100-yard mark for the sixth time in his last eight games.
The Blue Raiders (3-1, 1-0 C-USA) won their Conference USA debut over the Owls (1-3, 0-2 C-USA). Both schools are in their first seasons as members of C-USA after leaving the Sun Belt.