New Mexico State's Larry Rose III ran for 64 of his 229 yards to score a touchdown with 2:47 left in the second quarter, tying the score at 17. Justin Manton kicked a 22-yard field goal to give the Warhawks a three-point advantage before the break.
Louisiana-Monroe blocked a punt at the end of the third, and Mitch Lane recovered it to stretch the Warhawks' lead to 10. The Aggies were held scoreless in the second half.
Thomas completed 35-of-50 passes, and Kenzee Jackson finished with 108 yards on 13 receptions for Louisiana-Monroe (4-7, 3-4 Sun Belt).
Rose rushed for two touchdowns for the Aggies (2-9, 1-6). Tyler Rogers threw for 102 yards and one interception.
The victory snapped the Warhawks' six-game losing streak.