Farrell was knocked unconscious during Saracens' Premiership victory over Exeter Chiefs on Saturday and he was replaced immediately.
Return-to-play protocols dictate a concussed player must stand down for a minimum of 12 days, which could make the flyhalf a doubt for their first match against Argentina at Twickenham on November 6th.
"Owen Farrell will progress through his graduated return to play protocols at home," the RFU said.
Jonny May (dislocated elbow) and Henry Arundell (ankle) have also withdrawn from the England squad. Tom Roebuck has been called up for the first time while Adam Radwan and Henry Slade also return.
Arundell and prop Will Stuart (knee injury) are both travelling with the squad but will rehab in Jersey.
England also play Japan, New Zealand and South Africa next month.