Novak's kick with 3:21 left in fourth quarter capped a Chargers rally from a late 24-14 deficit, forging a 24-24 deadlock.
After Kansas City's Ryan Succop missed a 41-yard try at the end of regulation that would have won it for the Chiefs, Novak connected on a 36-yard try 5:30 into the extra period.
San Diego (9-7) then held off the Chiefs' final push to wrap up the AFC's playoff sixth seed with a fifth straight win to end the regular season.
Philip Rivers threw three touchdowns, going 22-of-33 for 229 yards with an interception.
Ryan Mathews amassed 144 rushing yards on 24 carries.
Chase Daniel tossed for 200 yards and a touchdown on 21-of-30 efficiency in his first NFL start.