The Argentine striker had only just returned to action last weekend after four months on the sidelines following knee surgery.
But after playing the first 45 minutes at the London Stadium, he was replaced by Phil Foden at the start of the second half with Foden netting an equaliser to cancel out Michail Antonio’s first half opener.
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And the City boss revealed he was waiting to discover the full extent of the injury to our all-time record scorer.
“It’s a muscular (injury). Hamstring, I think. Tomorrow we will know,” Guardiola revealed.
Aguero’s setback was the latest in a series of injury and illness issues to key players which have hampered our start to the new season
But Guardiola admitted it was a testing scenario which he and his staff had to deal with and work our way through.
“I am not complaining about that. I could complain about the first goal, I didn't say anything.
"The reality is we had four of five guys with COVID. We didn’t have time for regeneration,” Guardiola added.
“Our striker (Gabriel Jesus) was injured in the first game. Sergio was out for four months. Kevin was injured. Gundogan came back from COVID.
“To play every three days you need the whole squad. To not have the whole squad is more difficult.
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“I am not saying this is the reason why, I am just putting this on the table. It’s the reality.”
The result left City in 12th place in the table on eight points from five games – the lowest return at this stage of the season in six years.
For his part, Guardiola admitted it was a frustrating scenario, but he insisted the collective focus would not be deflected with attention now switching to Tuesday’s Champions League trip to Marseille.
“I would prefer to have the results. We have to anaylse where we are,” the boss added.
“It’s time to struggle for the injuries, the lack of preparation and the tough games we play so far. The players did absolutely everything.
“Now we recover and think of the next game in the Champions League (away to Marseille).
“We started really well. We conceded a goal from the first action they had. After we struggled in the first half. We couldn’t find the pass.
“We had chances at the end, three or four that we couldn't convert.”