However, Guardiola has now confirmed the tendon injury will see Aguero miss the Manchester derby at the Etihad on December 7.
"A few games, I don't know exactly," said Guardiola.
"He has a tendon problem in front - will be a few games out."
He added: "We will miss Sergio.
"We have had some problems with injuries but we will wait for him and meanwhile we have [Gabriel Jesus] and [Raheem] Sterling who can play in that position. We will live without him for a while."
Rodri and David Silva also had to be substituted, with cramp, but they are expected to be available for selection tomorrow after reporting no further issues.
2nd choice Striker Gabriel Jesus has been restricted to just four Premier League starts this term, but is likely to be drafted in for Aguero while he recovers from his tendon issue.
The Brazil forward insists he is ready to fill the void left in Guardiola's line up by a key performer, with it his desire to keep improving and stake a claim for a more permanent spot in the City team.
"I'm not happy because Sergio is injured," he told a press conference on Monday.
"I don’t like it when my friends are injured but I work hard every day. I’m ready to play and show every time that I want to improve. I’m ready.
"When I decided to come here I knew it would be hard because we have Sergio who is the top scorer in the club and scores every game. I knew this. But I have a chance to play with Pep, with top, top players here at a big club. So that is why I came, to enjoy and learn."
The Blues need a point to secure a place in the knockout phase of the competition, and a win would ensure they finish top of Group C, and so will be seeded for the draw for the last 16.
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