The diminutive Argentina striker stunned Old Trafford in April with a solo effort to win the game and Pellegrini is tipping Aguero to come good again at the Etihad Stadium.
Pellegrini said: "Sergio is very important, he is an incredible player, he makes a difference in every game he plays.
"He didn't do a very good pre-season because he has a lot of problems but now every game he is playing better.
"I am sure he will play a very good game on Sunday because Sergio always appears in important games.
"Every match against Manchester United is a special match. Of course it is very important but I don't work with just the confidence to play one match.
"Every match we win is confidence for me, for the club, for the players. Winning the derby is very, very important but it is not the last match of the season."
Vincent Kompany proved his fitness in the Champions League in midweek and David Silva has returned to training but Pellegrini was coy on making wholesale changes to his side.
He added: "We will see. We have seven matches in 21 days, it is normal to have some rotation."