The club’s all-time record goalscorer had only returned from a lengthy lay-off last week in the 1-0 victory against Arsenal and opened his account for the season in the midweek Champions League win over Porto.
Aguero started at the London Stadium but gave a subdued performance and did not reappear after the break, with Phil Foden introduced in his place.
Asked why the Argenine was taken off, Guardiola said: ‘Injury. No, I don’t know [what it is].’
The City boss subsequently confirmed the 32-year-old had sustained a hamstring injury and is therefore likely to miss upcoming matches against the likes of Marseille, Olympiacos, Sheffield United and Liverpool.
City have now won just two of their opening five Premier League fixtures this season and Guardiola was left frustrated by his side’s inability to find a winner after Foden had squared the contest shortly after his introduction.
‘We started really good, we concede a goal the first time they arrive,’ Guardiola added. ‘They defend so deep and we had the chance at the end to score the goal. Now we move forward.
‘We created enough. Their defenders were defending so deep so it’s difficult to find spaces, but we had the chances.
‘I’m not a guy who can predict the future. We’ve already dropped seven points, which is a lot. But we’ve struggled a lot for many reasons. We have to take things game by game and see what happens.’