The Argentina international had been a doubt for the game against Paul Lambert's men at Villa Park, after suffering a knock in the Manchester derby on Sunday.
And Pellegrini has confirmed the striker will definitely not be risked for the game, but suggested he could return in time for the UEFA Champions League tie with Bayern Munich on Wednesday.
"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," the City boss said on Friday.
"We will leave him for next Wednesday but he will be absolutely fine."
City sit third in the Premier League table after their 4-1 win over rivals Manchester United at the Etihad Stadium, having also enjoyed a 5-0 League Cup win over Wigan Athletic on Tuesday.
Pellegrini insists his players are focused on winning their fourth consecutive game in league and cup at Villa Park, rather than their trip to face Bundesliga champions Bayern.
"I am sure that nobody is thinking about Bayern Munich, we are all thinking about Aston Villa, we know it is a strong team playing at home so we need to play a very good game if we want to win, and we need to win," he continued.
"If we repeat what we did against Manchester United (they are) very near, but all the games are different, performances are different, squads are different so it's important that we see the same team (performance)."
The Chilean is also confident he can keep all of the stars in his squad happy with regular rotation.
"That (handling squad rotation) is the least problem," he said. "The important thing for a manager is when you don't have enough players to make rotations.
"All the players understand that we need an important amount of players – I say two in each position – because we have a lot of games to play from now until the end of the year."
