The Raptors have lost six in a row since their lone victory, which came Oct. 29 against Cleveland.
Thomas gave Charlotte a three-point lead with a pair of free throws with 12 seconds left and Stephen Jackson then stole the ball from Andrea Bargnani to clinch the Charlotte win.
Jackson led Charlotte in scoring with 20 and Gerald Wallace contributed 19 points and 14 rebounds.
Toronto was led by 23 points from Bargnani and 20 from Sonny Weems. The Raptors had an eight-piont advantage late in the third period, but could score just three points over the first 4 minutes of the fourth.