The San Francisco 49ers rallied for a 31-21 win over the San Diego Chargers as Colin Kaepernick knelt during the national anthem on Thursday night in San Diego.

Kaepernick, the 49ers' quarterback, was met by boos whenever he took the field.

Neither side used its regulars in the final preseason game for both teams.

With Blaine Gabbert presumed to be the 49ers' No. 1 quarterback, Kaepernick, who led San Francisco to two NFC title games, was believed to be fighting for a roster spot. Kaepernick completed 11 of 18 passes for 103 yards, capping a week in which he dealt with the controversy regarding his protest for civil justice.

San Francisco safety Eric Reid also took a knee with Kaepernick during "The Star Spangled Banner," which was played on the Chargers' annual Military Night.

San Francisco (2-2) trailed by 12 points going into the fourth quarter, then took a 24-21 lead after quarterback Christian Ponder's two short scoring runs. Running back Kelvin Taylor added a 10-yard touchdown run.

The Chargers (1-3) scored twice in the third quarter to take a 21-9 lead. Running back Kenneth Farrow rushed in from 6 yards before a 17-yard strike from No. 3 quarterback Mike Bercovici to wide receiver Isaiah Burse.

Kellen Clemens, who is beginning another season as the backup to Chargers quarterback Philip Rivers, played the first half, as did Kaepernick. Clemens was 11 of 15 for 113 yards.

The 49ers led 9-7 at halftime thanks to running back DuJuan Harris' scoring run and Phil Dawson's field goal. For San Diego, fullback Chris Swain had a 1-yard touchdown plunge.

Farrow rushed for a game-high 63 yards on seven carries. Taylor gained 56 yards on nine carries.