Charcandrick West got the Chiefs into a strong field position early on, but was held up short while trying to force his way into the endzone for the touchdown.
The Chargers struggled to get their offense going in the first quarter, but kicker Josh Lambo managed to get the home side on the board with a field goal early in the second.
The tight end could not keep hold of the ball though, with linebacker Manti Te'o breaking up the pass, forcing the visitors to settle for another field goal just before the break.
Both sides were forced to punt early in the third quarter as the two defenses continued to restrict their opponents, but Philip Rivers threw an interception to Justin Houston midway through the period, leaving the linebacker to run it back for a touchdown.
The Chargers put together a lengthy drive at the start of the fourth quarter as they desperately tried to get back into the game, with Danny Woodhead making a couple of gains for the hosts, before the drive stalled, forcing another punt.
Any hopes San Diego had of a late comeback were dashed on the Chiefs' next possession, though, as Spencer Ware took over the rushing duties to set himself up for a three-yard touchdown.
Ware was in again in the final two minutes after the Chargers were forced to punt once more, making a 20-yard dash through midfield before sneaking over from three yards out.
The result leaves the Chiefs second in their division with a 5-5 record, while the Chargers sit bottom with just two wins from their opening 10 games.