McGuire ran for 169 yards and two scores and Harris had 86 yards and three scores for the Ragin' Cajuns (8-4, 7-1 Sun Belt). Terrance Broadway completed 14 of 19 passes for 142 yards and also ran for a touchdown.
The Ragin' Cajuns trailed 23-21 at the break but came back to shut out Troy in the second half, scoring 21 straight points on two runs by Harris and one by Broadway.
Brandon Silvers threw for 272 yards and three touchdowns for the Trojans (3-9, 3-5).
It was the final career game for Troy coach Larry Blakeney who announced his retirement this fall. Blakeney's 24-season tenure was the second longest at an FBS school among active coaches behind Frank Beaner of Virginia Tech.