The Argentine will miss the first leg of the Champions League tie against Barcelona with a hamstring problem suffered in the 5-1 victory over Tottenham on Wednesday
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Aguero had made only one start since returning from a calf injury when he completed 90 minutes, scoring a hat-trick, in the FA Cup tie against Watford at the Etihad Stadium four days prior to the Spurs game.
But Pellegrini insisted he did not regret leaving the 25-year-old on the field to inspire the Premier League leaders to a come-from-behind victory against the Championship club.
"It wasn't a mistake because for us the most important thing is to win the match that we have to play," he said. "At that moment we were losing and it was important for Sergio to continue playing.
"Maybe if we were winning, he would have played 75 minutes so it was not an important amount. Maybe he played 10 or 15 minutes more, but I don't think that was directly related to his injury - I would make the same decision [again]."