Gates will sit out for the fourth time in six games.
Among the other Chargers inactives are linebacker Larry English, right guard Louis Vasquez and wide receiver Malcom Floyd. Randy McMichael is to start for Gates, Tyronne Green for Vasquez and Legedu Naanee for Floyd.
The 49ers reported no lineup changes.
Also Thursday, the Chargers signed linebackers Darry Beckwith and Brandon Lang from the practice squad to the active roster in time for the game.
Beckwith and Lang will be needed on special teams.
Information from The Associated Press was used in this report.