Sam Houston (11-9, 6-3) ran away and hid from the Lions in the second half after leading by only three, 26-23, at intermission.
The Bearkats opened the second period with a 16-4 run in the first six minutes and out-scored the Lions 41-23 for the half.
Britni Martin added 19 points, six rebounds and five assists to give SHSU two players in double figures.
"We didn't want to just hang around with them," Martin said of the second half turnaround. "We knew we were better than that, defensively. We came out focused on our defense, pushing the ball and running the floor. We got some easy buckets from steals and that really helped a lot."
Southeastern Louiusiana (7-14, 2-6) was led by Kelli Jenkins with 18 points and eight boards and Aja Gibson with 13 points and six rebounds.
The victory combined with a Texas State loss to Nicholls State put the Bearkats back atop the Southland Conference West Division standings.
Sam Houston out-rebounded the Lions 51-38 and out-scored Southeastern Louisiana 24-14 in the paint as Angela Beadle also produced double figure rebounds with 13.
Jasmine Johnson scored eight points and Beadle totaled six.
"We run the floor when we're on and we just do what we can to help our team," Johnson said. "Defensive pressure is something we work on every day. We work on just going hard, getting after it and not letting the other team get what they want."
Thomas, who leads the Southland in rebounding, has 12 double points and rebound performances to her credit this season.
The two teams exchanged leads five times in the first half but the Lions never led by more than two points. After a lay-up by Thomas to make the score 12-11 with 9:46 to play in the first half, Sam Housotn never trailed again.
Sam Houston returns to action on Wednesday night, traveling to UT-Arlington. The Bearkat women will be back in Johnson Coliseum next Saturday against Texas A&M-Corpus Christi.