Thomas was back in the Clippers' lineup after missing two games because of a family emergency in New Jersey, but Corey Maggette sat this one out due to a bruised tailbone and Aaron Williams was sidelined by a right calf strain.
Chris Kaman led Los Angeles with 19 points and nine rebounds.
Mike Bibby had 28 points for the Kings, but failed to score in the final 3:55 and committed a costly turnover with less than a minute to play. Both teams combined for 57 fouls.
Bibby made eight of 12 shots in the first three quarters -- four of them from 3-point range -- but the rest of the team was 15-for-45 from the field. The Clippers led by as many as 10 points midway through the third quarter before Bibby's short running bank shot with 10 seconds left in the period put the Kings ahead 69-67.
The lead changed hands four more times before Clippers point guard Brevin Knight scored his first points of the game on a 20-foot fadeaway jumper and converted the free throw to give Los Angeles a 78-75 lead with 8:28 remaining.
The Kings tied the score three times after that, the last time on a pair of free throws by Kevin Martin with 1:31 left. But they never could get the lead back. Bibby made a bad pass out of bounds with 32 seconds left and Thomas made him pay with his clutch shot on the ensuing possession.
The Kings had one more chance, when Bibby drove the lane on an inbounds play and kicked it out to John Salmonds. But his jumper was partially tipped by Cuttino Mobley as time expired.