Rivers' 22-yard scoring strike to Keenan Allen early in the second quarter put the Chargers ahead to stay and Novak connected on kicks of 31, 33, 34 and 50 yards in the victory.
Rivers completed 22-of-33 passes for 237 yards without an interception and Ryan Matthews ran for 102 yards on 22 carries for San Diego (3-3), which bounced back from a 27-17 loss to Oakland last week.
The Chargers' defense held Indianapolis to just 267 yards of total offense in the victory.
Andrew Luck went 18-of-30 through the air for 202 yards with an interception for the Colts (4-2), whose three-game winning streak was snapped.
Adam Vinatieri connected on three field goals in the loss.