The City striker hobbled out of the champions’ 2-1 Premier League win over Chelsea at the Etihad Stadium on Saturday, and Guardiola is unsure how long the Argentine will be sidelined but is resigned to his missing the visit of Manchester United on December 7.
The City boss, speaking at a press conference to preview Tuesday’s Champions League clash with Shakhtar Donetsk, said: “He will be out a few games. I don’t know exactly, for a few weeks he will be out.”
Asked if the 31-year-old would miss the derby, Guardiola said: “Yes.”
Pushed further on the matter, he added: “Maybe we will have a miracle but I don’t think so.”
Aguero’s absence will mean opportunities for Brazil striker Gabriel Jesus. The 22-year-old has scored five goals this season but has started only eight times due to the presence of Aguero.
Jesus, who was sat alongside Guardiola, said: “I am not happy because Sergio is injured. I don’t like it when my friends are injured but I work here every day and I am ready to play.”
Jesus admitted it was frustrating to be on the bench regularly but he is not complaining.
“When I decided to come to City I knew it is going to be hard because we have Sergio, who is the top scorer of the club and he scores every game,” he said.
“I know this but I think I have a chance to play with Pep, with top players here and at great big club, so that is why I came, to enjoy and learn.”
Guardiola was also asked about the future of his highly rated assistant Mikel Arteta, who has again been linked with his former club Arsenal.
Arteta was touted as a potential successor to Arsene Wenger at the Emirates Stadium last year and his name is again being put forward with current Gunners boss Unai Emery under pressure.
“Of course he (Arteta) will be a manager sooner or later,” said the City boss. “We are going to finish the season but in future I don’t know what will happen.
“I’d like him to stay with us as much as possible.”
City, five points clear at the top of Group C, are under little pressure heading into Tuesday’s match.
A draw will be sufficient to secure their place in the last 16 for a seventh successive year with a game to spare.
Guardiola said: “The position we have is good … Tomorrow we have the chance to close the group stage. We have to do our best to go to Zagreb (for the last game) with the job done.”