The Citizens sealed their place in the last 16 after claiming a 5-2 win over CSKA Moscow at the Etihad Stadium.
It is the first time that City have managed to get out of the group stages and Pellegrini was glad to have qualified with two games left to play.
"It is the first step but it's an important one as the team has not qualified before. We have done that now," BBC Sport quotes him as saying. "I always want to score goals but at least one of the CSKA goals was very easy for them. They didn't have too many chances but scored two goals. Today we conceded soft goals again.
"The most important thing was that we can play the last two games of the group and try to come top. Then we can see in February who we get and anything can happen in the knockout stage. David Silva and Fernandinho both have small problems so we will see tomorrow what the doctor says."
Manchester City will host Viktoria Plzen in their next Champions League fixture on November 27.