Previewing Saturday evening’s visit to Goodison Park, the Blues boss explained the England defender suffered concussion and will be unavailable for selection against his former club.
Guardiola also stated he has no new injury concerns, adding that Sergio Aguero is ‘much better’ following his knee injury.
“John Stones has concussion in his head from the last game of the international break," he told press.
“He feels really good but the rules say he must take seven days off so he is not available. The other ones are okay.”
On Aguero, who sustained a knee injury in training before the Blues’ clash at Stoke, he continued: “He is much, much better.
“We will see tomorrow if he is involved.”
Everton are the only Premier League team to have emerged unbeaten from the Etihad Stadium this season, holding City to a 1-1 draw - as they did the year before.
The Blues' last visit to Goodison Park heralded a 4-0 defeat and Guardiola expects a similarly tough test this weekend.
“(Under Sam Allardyce), Everton have been good,” he said. “The results are better. Especially at home, the results are so strong.
“Everton at home last season was one of the best performances and we drew.
“I didn’t think we played that badly but when the result happens, you have to accept it. I think this season, the results have been much better.
“Goodison Park is always a tough ground.”