Aguero to miss Aston Villa game
Aguero scored twice before being withdrawn after 86 minutes as City thrashed Manchester United 4-1 at the Etihad Stadium.
No injury was indicated at the time and nothing seemed untoward when he was then rested for the midweek Capital One Cup win over Wigan.
But Pellegrini has now revealed a problem and does not want to take the chance of playing Aguero at Villa Park on Saturday.
Pellegrini said: "Aguero finished the last derby in the last play with a small pain, I think it was nothing important but I think it was a risk for him to play three games in the same week.
"We will leave him for next Wednesday but he will be absolutely fine."
Playmaker David Silva, who has missed the last four games with a thigh strain is also not fit to return at the weekend but will be assessed ahead of the Munich game.
The European champions visit Eastlands on Wednesday in the second round of games in Champions League Group D.
Pellegrini said: "We will see in the week."
Pellegrini insisted the looming game against Pep Guardiola's Munich would not affect the players' thinking for the trip to Villa.
City laboured in a goalless draw at Stoke immediately prior to their last Champions League outing against Viktoria Plzen a fortnight ago.
Pellegrini had made six changes for that game and Potters boss Mark Hughes suggested City may have paid the price for prioritising the wrong game.
Pellegrini said: "I am sure nobody is thinking about Bayern Munich. We are all thinking about Aston Villa.
"We know it is a strong team playing at home. We need to play a very good game if we want to win and we need to win away now."