Thomas helped the Kings go on a 22-6 run to start the second quarter to bring Sacramento (5-2) back from a 10-point deficit.
The Clippers led 30-20 after the first quarter but couldn't maintain the pace. They shot just 26.7 percent from the floor in the second quarter and found themselves trailing the rest of the way.
DeMarcus Cousins scored eight points for the Kings in the first quarter but sat out the second with three fouls. He returned in the second half and finished with 20 points. Marcus Thornton added 17 points for the Kings.
Chris Paul led the Clippers (5-3) with 23 points.