-...denying him the chance to become the first player in Premier League history to score six in a game ... but Pellegrini revealed he had been carrying a knock.
Pellegrini said: "He had a serious kick from Wednesday in Germany
He was having some treatment during half-time.
"To give him more minutes, maybe he would have scored one or two goals more, but we need more to take a precaution about his kick because he could get injured."
When asked more about the nature of his treatment at the interval, Pellegrini said: "Maybe it was very good treatment!
"He had a kick in his hamstring, so it was important just to relax him a little bit because he was not 100 per cent comfortable."
Pellegrini was convinced Aguero, City's top scorer last season with 32 goals in 41 appearances, would soon come good.
Aguero did score against Chelsea in the second game of the season but then had a setback after suffering a knee injury in a challenge from Crystal Palace's Scott Dann last month.
Pellegrini said: "I am very happy for Kun. He deserves it. He is always a player who makes a difference.
"For different reasons in the last few games he missed important chances, but he was calm. That was very clever from him. To see him play at the level he played today, not only must I be happy but all the fans because he is a different player."