The manager was also full of praise for Belgian midfielder Kevin de Bruyne after he scored a late winner against Sevilla.
The Belgian defender started their 2-1 win over Sevilla on the bench on Tuesday evening, coming on as a late substitute as City looked to shore up the defence.
The defender has been absent for several weeks with the latest in a series of niggling injuries, but recently played for Belgium in their European Championship qualifiers after returning to training.
In his absence Nicolas Otamendi and Eliaquim Mangala have been started in the heart of the defence and Pellegrini says they deserved to continue after their recent displays.
“Vincent is just coming back from a month out with injury and that’s why he started as a substitute,” he told mcfc.co.uk.
“Nicolas Otamendi and Eliaquim Mangala have been playing well and were in the side that beat Newcastle 6-1 and Bournemouth 5-1 so they deserved to continue.”
The manager was also keen to praise young midfielder Kevin de Bruyne after he scored the late winner against the La Liga side.
Secured for big money from Wolfsburg this summer, there is big pressure on the Belgian to produce the goods to justify his lofty price tag, and so far he has made an impressive start to his career at the Etihad.
And Pellegrini says they knew he was the perfect player to bring to the club.
“We bought Kevin because we knew is a very creative player who can score and create goals and in that respect he was the perfect player to bring to our club,” he added.
“We tried to make some changes which is why we put Kevin up front with Yaya and fortunately, between them, the created the second goal. It is important that we won this game with the derby to come on Sunday.”