LT Joe Staley (shoulder), G Adam Snyder (quadriceps) and third-string quarterback Troy Smith (abdomen) were limited in practice.
Manusky said LB Takeo Spikes is sharing some snaps with rookie NaVorro Bowman in an effort to keep Spikes, a 13-year veteran, fresh.
CB Will James, who returned from a sprained ankle last week, will continue in his role as the No. 3 CB against the Raiders. James has supplanted Tarell Brown.
Johnson said RB Brian Westbrook, who has four touches in five games, will become more involved in the offense. "As we go forward, I think his role will increase and he will help us out," Johnson said.