A Citizens XI without Fernandinho, who was ruled out on the day of the game, and top goalscorer Sergio Aguero among others, lost their 100% home record in the Premier League this season courtesy of a Branislav Ivanovic goal at the Etihad Stadium.
"I think that of course Fernandinho is a very important for us, but you must add, Sergio Aguero, Samir Nasri and Javi Garcia - and that is too much against an important team like Chelsea," he told reporters. "We lost against a good team and they played very well, but we deserved a draw because we had the chances to score, but we didn't take them.
"Chelsea played defensively, and they concentrated on defence, but a lot of chances. I don't think they had possession of the ball in the midfield, I don't think that's why we lost the game. I think we put our best players who were available, and that was not the issue.
"We have five or six less players because of injury and so I don't think this defeat will have a psychological effect on the team, because we know they were the only options we had available."
Pellegrini has revealed that Fernandinho will miss three to four weeks with a muscle injury.