The 21-year-old suffered the injury in Spain's 2-1 UEFA Nations League semi-final victory over Italy but managed to play through the pain for 84 minutes in the 2-1 defeat by France in the final.
Scans conducted upon Torres's return to Manchester revealed a small fracture, and Guardiola suggested it could be a long wait before he plays again.
"Torres will be out for two months and a half, three months," Guardiola said.
"Except Ferran, the rest of the team are OK. The injury is the fourth metatarsal."
Guardiola considers Spain boss Luis Enrique blameless, saying he had full trust in his former Barcelona team-mate.
"The injury can happen here, at home, with the national team. I know perfectly Luis Enrique, he treats all the players as good as possible," Guardiola said.
"He doesn't want Ferran to get injured. They try to take care, sometimes it happens. It happened with Belgium with Kevin [De Bruyne], Phil [Foden] with England.
"It would be better not to happen but unfortunately it happens. He will spend a few weeks in Spain and then come back and recover hopefully in two, three months."
Guardiola said he was "delighted" Oleksandr Zinchenko and Ilkay Gundogan had recovered from knocks and were back in training, ahead of the home game against Burnley in the Premier League on Sunday (AEDT).
However, Brazil internationals Ederson and Gabriel Jesus will miss the Burnley game, having been on FIFA World Cup qualification duty with their national team on Friday (AEDT).
"They played in Brazil yesterday, they cannot fly back [in time]," Guardiola said.
Asked if they would be available for the UEFA Champions League game against Club Brugge on Wednesday (AEDT), Guardiola said: "Maybe, I don't know that yet."
Torres is now certain to miss a long stretch of games, including the first Manchester derby of the season at Old Trafford on 7 November (AEDT), and seemingly the rest of City's UEFA Champions League group games.
It is bad luck for a player who enjoyed a fruitful start to the season, having been converted into a centre-forward by Guardiola.
Torres leads City in the Premier League this season for goals (two, level with Jesus), minutes per goal (152.5), expected goals (2.01) and shots (13, level with Gundogan).
With Torres and Jesus absent in the short term, Guardiola will have to look elsewhere for central attacking options. Foden and De Bruyne are not natural forwards, despite both players regularly being deployed in a false nine role.