The Argentina star hit all four goals for City - as well as missing a penalty - to preserve the champions' run of fine recent form over the north London club.
Christian Eriksen equalised Aguero's early opener, but the 26-year-old took the game beyond Mauricio Pochettino's men with a virtuoso display up front.
Despite the dominant scoreline, Pellegrini remained concerned by a few sloppy mistakes from his side - claiming he would not have been surprised by a 7-3 result.
But the Chilean was happy to share praise around his entire selection after coming back from international week in good form.
He said: "I think it was a very amusing game especially for the fans because we won 4-1, but I think the score could have been 7-3.
"Both teams had clear chances to score I think that's important for the fans. I always say it's important to be an attractive team, but maybe also not to make so many mistakes, especially with excess of trust with the ball at our feet.
"But it's very important to win this game after the international break. It's very difficult when you don't have the players during the week to work, so I'm very happy with it.
"First of all I think when we win a game it's not just for one for two players I think the whole team had a good performances. Of course when you score four goals as Kun [Aguero] did or make two saves as Joe [Hart] did, it's very important
"I think that we are not fair to not talk about James Milner or Jesus Navas or [Vincent] Kompany or [Bacary] Sagna."
Pellegrini also confirmed that Frank Lampard would not travel to Moscow for City's UEFA Champions League tie on Tuesday after picking up a knock.
