Thomas hit two free throws with 40 seconds left to extend Texas A&M-CC's lead to 67-60.
Thomas was 10 of 13 from the free throw line and his teammates were just 9 of 20.
John Jordan made seven of his 13 shots and had 18 points for Texas A&M-CC (11-8, 6-1 Southland Conference).
Onochie Ochie led SE Louisiana (5-14, 2-4) with 15 points and eight rebounds. Daniel Grieves had 14 points and Zay Jackson 13. The Lions were just 2 of 26 from beyond the arc.
Ochie's three-point play capped SE Louisiana's 9-2 run for a 50-48 lead with 10:01 left, but Jordan answered with one of his own to start a 9-0 run.