Sam Houston (4-4) trailed by as many as 13 points in the first half, but rallied to lead by two at halftime.
After a pair of lead changes late in the game, Thomas put the Bearkats ahead to stay 46-45 with a layup with 4:16 to play. Thomas hit another jumper with 2:07 to put the Kats up five. Britni Martin and Chanice Smith each knocked down a pair of free throws in the final minute to keep the lead alive.
Eight of Thomas's 12 points came in the final eight minutes of the game. South Alabama (7-5) was paced by Camille Reynolds with 10 points.
The Jaguars hit their first three treys to build an early 21-8 nine minutes into the contest. But the Bearkat defense allowed South Alabama to hit only four of their next 27 three-pointers to close out the game with 25 per cent shooting overall from the field and 23 per cent from beyond the arc.
"I was really proud of the way we keep fighting when we got down early," head coach Brenda Nichols said. "We played some tough defense when we had to and finished strong."
Martin and Smith each added 11 points for Sam Houston. The Bearkats were 16-of-53 from the field fo 30 per cent shooting but out-rebounded the Jaguars 46-41 and out-scored USA in the paint 16-12.
Jasmine Johnson scored eight points and Jasmin Wiley added seven more for the Bearkats.