With Vincent Kompany back from his latest calf problem and Aymeric Laporte signed from Athletic Bilbao this week, Guardiola opted to give Stones extra recovery time after missing the midweek 3-0 win against West Bromwich Albion due to illness.
"He has a bit of a problem in the knee and I prefer for him to rest, to recover a bit," the City manager told the Manchester Evening News. "It is a little bit painful.
"I have Vincent back and Aymeric Laporte is already here. I decided not to use [Stones] today, let him recover and come back better against Leicester and Basel."
Guardiola revealed prior to kickoff against Burnley that his players had been given four days off and will not have to report back for training until Wednesday afternoon.