The Argentine striker has not played since 22 June, when he suffered an injury to his left knee in the 5-0 win over Burnley during the Premier League restart.
He immediately travelled to Barcelona, where he was operated on by renowned knee specialist Dr Ramon Cugat, which meant he missed the final 10 league games and two Champions League ties.
“We knew that the injury was difficult,” he said at his pre-match press conference.
“He is doing the job, in maybe one month or two months he will be ready.”
Should the predicted two-month time frame prove correct, Aguero could potentially miss the upcoming home games against Arsenal on 17 October and defending champions Liverpool on 7 November.
It would mean City have been denied the services of our record goalscorer for five months, but Guardiola says it is important Aguero is given time to build up his fitness so he returns to action in the best possible shape.
“He has to come back on the pitch and regain the physical condition,” added the boss.
“Sergio was out for a long time and Sergio is not a guy who regains the physical condition quick so I think in one month or two months he will be ready.”
Watch exclusive CityTV features, including the new Kevin De Bruyne documentary, with a CITY+ subscription.