Elton Brand added 13 points and 13 rebounds for the Clippers, who were playing their third game in as many days after going 1-1 in the Lakers' annual Staples Shootout.
The Clippers never trailed despite committing 20 turnovers and playing without injured guard Sam Cassell (strained left calf) center Chris Kaman (strained left hamstring) and center Zeljko Rebraca (back).
Ray Allen scored 19 points for the Sonics, who were short-handed because of injuries to Danny Fortson (left knee) and Kareem Rush (groin strain). Rashard Lewis had 13 points and nine rebounds.
Allen scored seven straight points during a 14-0 run, which ended with a 3-pointer by Earl Watson and a layup by Nick Collison as the Sonics pulled into an 80-all tie with 3:07 to play. But Brand put Los Angeles back in front 19 seconds later with a layup, ending a 4:03 span between field goals for the Clippers.
Quinton Ross hit a 17-footer from in front of the Seattle bench to give Los Angels an 84-80 lead with 48 seconds left. Lewis came back with a dunk at the other end and the Clippers lost possession on a shot clock violation, giving the Sonics the ball with 13.2 seconds on the clock.
Allen misfired on a 3-point shot over Ross and Thomas grabbed the defensive rebound before Mobley clinched it with a pair of free throws.
Thomas, who was 1-for-11 from the field in Thursday night's one-point win over the Lakers, led the Clippers to a 49-34 halftime lead with 13 points -- including a 3-pointer that capped a 9-0 run at the end of the second quarter. They opened the game with a 15-4 run, as Allen picked up two fouls in the first 2:35 and the Sonics made only one of their first 11 shots.
Allen returned to the floor with 7:39 left before halftime and Seattle down by six. But the Sonics, who have lost four straight after routing Portland in their preseason opener, never could overtake the Clippers and finished the game shooting 35.5 percent from the field.