Aguero set City on their way to a 5-1 win at 10-man Tottenham on Wednesday before he limped off with a hamstring problem just before half-time.
Yaya Toure, Edin Dzeko, Stevan Jovetic and Vincent Kompany were also on target at White Hart Lane as City surged to the top of the Premier League, but the victory was soured somewhat by striker Aguero departing hurt, having only just overcome a calf complaint.
Pellegrini, though, knows that he has the firepower at his disposal to cope without the Argentina international.
He said: "We tried not to depend on one player. Sergio has just come back from another injury and when he didn't play, it was the turn of (Alvaro) Negredo and Dzeko.
"We will always miss Sergio because he's a top player and want him as soon as possible in the team. But at the moment with Jovetic, Dzeko and Negredo, we have very important strikers."
Pellegrini insisted Danny Rose's red card was not a turning point when City led 1-0. Rose was dismissed after he was adjudged to have fouled Dzeko in the box and Toure made no mistake from the spot.
The Chilean said: "I don't think that was the big decision because I think before the red card we missed at least five clear chances to score in the first half and if we review the first 45 minutes, I don't remember one chance for Tottenham so I think our team was the best team from the beginning.
"I don't analyse the referee because I am not the referee.
"I repeat that the sending off was not the thing that changed the game."
Victory over Tottenham made it eight wins in a row in all competitions for City.
"Yes of course (I'm happy)," he added. "Not only because we are top of the league, but because I think the team played very well today.
"We played against a very good team in a very good moment. It's not easy to score here in their own stadium.
"We also defended very well so the performance of the team was complete."
