The Champions League holders booked their place in the last 16 of this season's competition as they breezed to a 3-0 win over Swiss side Young Boys on Tuesday night.
The only negative from Tuesday night's triumph at the Etihad Stadium saw Stones go off at half time. Nathan Ake was brought on to replace Stones.
Guardiola revealed after the match that Stones was experiencing the same hip injury that kept him sidelined for the best part of six weeks at the start of the season and that the England international won't be back any time soon.
"John felt it again. I feel so sorry for him," Guardiola said after the match.
"It's a big loss for us. John is so important for what he does. But recover and the season is long; he will be back stronger.
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"I think he will be out for a while."
Erling Haaland put City ahead with a penalty on 23 minutes, while Phil Foden made it 2-0 in stoppage time at the end of the first half.
Haaland then got his second and City's third with a fierce strike into the top corner on a night that also saw Young Boys captain Mohamed Ali Camara rush over to the Norwegian at half time to get his match worn shirt off him.