The team announced the firing Monday, one day after it fell to 0-3 and was beaten 31-10 at Kansas City. San Francisco has scored 38 points, second fewest in the NFL behind Carolina.
Mike Johnson will move from quarterbacks coach to offensive coordinator. Offensive assistant Jason Michael will take over as quarterbacks coach.
The 49ers were considered a favorite in the NFC West this year, but their offense has stalled, plagued by turnovers and a weak running game.