Bortles scored from 1 and 15 yards, with his second TD -- in the final seconds of the third quarter -- giving the Knights (11-1, 8-0 AAC) their eighth consecutive win.
Bortles ran 10 times for 31 yards and completed 24-of-35 passes for 242 yards. Jeff Godfrey caught five passes for 62 yards.
Central Florida clinched the American Athletic Conference's automatic BCS berth Thursday when Louisville beat Cincinnati.
Southern Methodist led 10-3 at halftime but could only add a Chase Hoover field goal to its total in the second half. Neal Burcham started his second consecutive game at quarterback in place of injured Garrett Gilbert and completed 24-of-34 passes for 222 and one touchdown.