It was the second victory in a row and third consecutive at home for the Bears (3-5).
"We're trying to get a rhythm and momentum going for us," said Thomas, who had been sidelined because of a sore foot.
The momentum, however, nearly turned toward the Chargers when backup quarterback Doug Flutie, 10 days after his 41st birthday, replaced Drew Brees in the fourth quarter.
Flutie connected with Tim Dwight on a 22-yard pass play and rushed for 17 yards to set up LaDainian Tomlinson's three-yard touchdown run that pulled San Diego within six with 9:13 to play.
The Charger defense got Flutie the ball back with plenty of time left. But Bear cornerback Charles Tillman downed the punt at the one, and Flutie couldn't get the Chargers (1-7) beyond the 17.
Thomas all but ended any hope of a comeback with his own six-play, 21-yard drive, capping it with a one-yard scoring run.
Chris Chandler, Chicago's 38-year-old quarterback, who had one pass intercepted, completed 21 of 30 passes for 224 yards.
Flutie completed eight of 11 for 70 yards. Brees, who had one pass intercepted, completed seven of 15 for 49 yards and had a passer rating of 26.8.
Coach Marty Schottenheimer said the quarterback switch "was a decision that was made to see if we could get a spark. It did some more than that.".
Schottenheimer hasn't decided who will start next week against Minnesota, but Brees has Flutie's vote.
"The bottom line is Drew's the starter and I'm his backup," Flutie said. "It's my job as the backup to come in, try to spark the team when I can, rally the troops."