The England international had only just returned from a hip injury but was forced off at half-time during Tuesday’s win over Young Boys BSC in the Champions League.
Manager Pep Guardiola is confident that the 29-year-old has not suffered a particularly serious knock but is unsure if Stones will return in time for the visit of Liverpool after the international break.
“The doctor said to me it's not as bad [as first thought], but I don't know. When he's going to be fit again he'll come back,” said the City boss on Friday.
Manuel Akanji, however, is available and he starts alongside Ruben Dias at the back.
The Swiss international pulled up during the warm-up with a back problem on Tuesday but trained on Friday before the journey to west London.
Erling Haaland started in the week despite a recent knock to the ankle and leads the line once again, with Kevin De Bruyne and Sergio Gomez the only long-term worries for City to contend with.
On De Bruyne, Guardiola added: “I spoke to him two days ago and he feels really good but he isn't training with us, not running much.
“I think, I don't know, these kind of injuries it's better not to put pressure. When he feels good and the doctors are confident we can take the next step.
“You don't want to go too early and have to go back again. Kevin was a tough injury, surgery, so step by step.”
Jeremy Doku unsurprisingly keeps his place in the side, after a strong run of form, with Julian Alvarez, Phil Foden and Bernardo Silva all starting too. Jack Grealish has to settle for a place on the bench.
Starting XI: Ederson, Walker, Akanji, Dias, Gvardiol, Rodri, Bernardo, Foden, Doku, Alvarez, HaalandSubs: Ortega Moreno, Carson, Phillips, Kovacic, Grealish, Nunes, Bobb, Lewis
Time and date: 4.30pm GMT on Sunday November 12, 2023
Venue: Stamford Bridge