The Argentinian suffered a muscular problem as he tried to recover match fitness following a knee injury in Saturday’s draw against West Ham in the Premier League.
Aguero, who was playing just his third match since June, was withdrawn at half-time and Guardiola is hoping the 32-year-old returns soon.
Guardiola said: “When you are four or five months out (with) knee problems, always you have a risk when you come back of injuries.
“We tried to handle it as well as possible, just 50-55 minutes a game but it was not enough to get fit for the next games. He will be back as soon as possible.”
Aguero joins Gabriel Jesus, Benjamin Mendy, Nathan Ake and Fernandinho on the sidelines.
The positive news for City is that defender Aymeric Laporte was fit enough to travel to Marseille for Tuesday’s Champions League clash after a knock.
Guardiola said: “Kevin (De Bruyne) is back again and played a few minutes against West Ham. Aymeric is back too, Nathan is so close. Gabriel is close – one week to 10 days to come back. The rest will be two or three weeks.
Asked if he had a clear idea of how long Aguero might be out, Guardiola said: “It depends on the injury. When it is minimum it will be 10-15 days. If it is longer it will be three weeks to a month. I don’t know.”
