The centre-back missed our Carabao Cup defeat to Southampton on Wednesday and will not be fit enough to return to face United.
Though there are no other reported injury concerns, the loss of the in-form Stones is undoubtedly a blow for the Blues.
“Stones is not ready,” said Guardiola. “I think everyone else is fit.”
That, in turn, suggests Ruben Dias is nearing full fitness, with the Portuguese defender absent since the World Cup.
Guardiola says the performance against Southampton was something that can happen when a team has won has much as City have in recent seasons.
The 2-0 loss at St Mary’s saw an off-colour City fail to register a shot on target, but the boss is hopeful it was no more than a rare blip.
“What happened didn’t surprise me, we tried to avoid it,” he said.
“It happened because we have won four Premier League titles in five years.
“The Carabao Cup - they have to show me consistency and this was our strength in previous seasons - but after back-to-back games (against Chelsea), we were not able to go there and be ourselves.
“Not (necessarily) win games – just be ourselves.
“I was concerned (the Southampton performance) could happen, it has happened and hopefully it won’t happen again.”
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