The Chargers kept quarterback Andrew Luck and the Colts out of the end zone, limiting them to three Adam Vinatieri field goals.
San Diego quarterback Philip Rivers went 22-for-33 for 237 yards and threw the game's lone touchdown pass as San Diego (3-3) bounced back from a disappointing loss to the Oakland Raiders a week ago.
Indianapolis (4-2) saw their three-game winning streak end.
Luck connected on 18 of 30 attempts for 202 yards, but he was hurt frequently by dropped passes. He was also picked off by cornerback Derek Cox with 1:07 remaining to seal the outcome.
San Diego finished with a large advantage in time of possession (38:31-21:29). The Chargers gained 374 total yards while limiting the Colts to 267 total yards.
Chargers running back Ryan Mathews gained 102 yards on 22 carries. Team mate Keenan Allen, who scored the game's only touchdown, made nine receptions for 107 yards.
Neither team scored a touchdown in the second half, but the Chargers drove for three Novak field goals.
In the first half, a 12-play, 74-yard drive, draining more than six minutes off the clock, ended with Rivers hitting Allen on a 22-yard scoring pass for a 7-3 lead at 12:02 of the second quarter.
On the Chargers' next possession, Rivers guided his team on a 17-play, 79-yard drive, resulting in a 31-yard field by Novak with 1:41 left for a 10-3 advantage.
San Diego possessed the ball for 18 minutes of the half compared to 12 for the Colts.