The Chargers had chances to take a big lead early. Instead, they settled for Cameron Dicker field goals after reaching the San Francisco 29, 7 and 21.
As it is, Los Angeles leads the 49ers 16-10 at halftime of Sunday Night Football.
Chargers quarterback Justin Herbert left the game for a concussion check after taking a helmet-to-helmet hit from Dre Greenlaw on a scramble with 30 seconds left in the half. Officials ejected Greenlaw from the game.
Chase Daniel replaced Herbert and threw two incompletions and took a sack before Dicker kicked a 40-yard field goal on the final play of the half.
It is not yet known whether Herbert will return to the game.
Herbert completed 14 of 21 passes for 161 yards and a touchdown, which came on a 32-yard throw to DeAndre Carter. Carter has three receptions for 70 yards.