England defender Stones picked up a muscle injury in the 3-0 win over Young Boys having only recently returned to the team after being out since August.
However, the City boss revealed that the issue may not be quite as bad as first feared.
“He is injured,” confirmed Guardiola at his Friday press conference.
“He is not ready for tomorrow and we will see after international break. I don’t know (whether he will be ready) for Liverpool.
“The doctor says it's not as bad (as first thought), but still I don’t know.
“When he is going to be fit again, he will be back.”
Asked if Josko Gvardiol could fill Stones’ unique role in the side, the boss added: “Maybe. Still he didn’t prove it in the training sessions and drills that we do to see how he moves in central area.
“I haven't seen it yet. (but he is) 21 years-old, so maybe.
“The fact John can do it is because we've been together for eight years.
“Josko is just two or three months here, so we need more time.”
He said: “Manu trained today and will travel. He is available for Sunday.”
And there was more positive news regarding Kevin De Bruyne who has been absent since August.
Guardiola revealed the Belgian is 'feeling good', but is still a few weeks off returning to full training.
“I spoke with him and he said he feels really good,” said Pep,
“He’s not training with us yet and I don’t know when he will. I would say he's in the last phase before he trains with us again.
“I think (that could be soon), but I don’t know. This kind of injury… it’s better we don’t put pressure on him
“If the physio says next step, next step…no pressure.
“Recover, it's not necessary to take the wrong or bad decision and then you’re back (where you were) again.
“Kevin’s was a bad injury with surgery, so it’s step by step.”