Feyi-Waboso was forced off at half-time during England's 45-22 win over Australia at Twickenham on Sunday.
He sustained the ankle injury following a hip-drop tackle from Angus Bell, who received a yellow card for the incident.
Feyi-Waboso was spotted wearing a protective boot after the final whistle.
The 23-year-old Exeter wing's absence is a major blow to England boss Steve Borthwick after his dynamic first-half display against Australia.
In 40 minutes of action, statistics showed Feyi-Waboso made 113 metres from eight carries, beating seven Australian defenders - figures unmatched by any other England player.
It is the latest fitness setback for Feyi-Waboso, who has been limited to 17 caps since making his debut in the 2024 Six Nations because of shoulder, hamstring and concussion issues.
Adding to Borthwick's problems, Seb Atkinson (hip), Ollie Chessum (shoulder) and George Furbank (groin) are all set to miss Saturday's clash with Japan.
Meanwhile, Tom Curry will play no part in the November fixtures after aggravating a hip problem in training last week.