Aguero scored twice before being withdrawn after 86 minutes as City thrashed Manchester United 4-1 at the Etihad Stadium.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 the Etihad Stadium on Wednesday in the second round of games in Champions League Group D.
Pellegrini said: "We will see in the week."