The Argentina striker suffered a knee injury in a challenge from Crystal Palace's Scott Dann in Saturday's 1-0 Barclays Premier League win at Selhurst Park on Saturday.
Aguero did not train with the rest of the squad ahead of Tuesday's European encounter at the Etihad Stadium and Pellegrini later revealed he would not play in the match.
Speaking at his pre-match press conference, Pellegrini said: "Sergio is not fit for tomorrow
He has a kick in his knee
It is difficult for him."
Aguero, last season's top scorer, could return for Saturday's Barclays Premier League clash with West Ham.
Pellegrini said: "I hope so but we must wait
We will see this afternoon how long it will be."
On the positive side, David Silva and Raheem Sterling, who missed the Palace game with ankle and hamstring problems respectively, did both train and will be expected to be fit.
Samir Nasri and Fernandinho both sat out the full session because of minor knocks but Pellegrini said he hoped "both will be 100 per cent fit tomorrow".
Source : PA
Source: PA