A Sergio Aguero hat-trick saw City to a 3-0 win over Chelsea in the Premier League on Saturday as Pellegrini's men, perhaps momentarily, moved into third.
City are still looking to seal a top-four finish and have a busy run of fixtures ahead of them late in the season.
However, Pellegrini said it would be down to the individual requirements of the games if he altered his side, not with an eye to Madrid ahead of the first leg on April 26.
"If I will be refreshing maybe some positions in the next game, [it's] not because I'm thinking of Real Madrid," he told reporters.
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"It's because between now and the end of May we need to play eight games in one month.
"It's important to make substitutions, but not thinking about Real Madrid."
Pablo Zabaleta was taken off midway through the second half at Stamford Bridge and was unhappy with Pellegrini's decision.
The Chilean, however, said he acted in the best interests of his team, adding: "Of course he was upset, it's my duty in the moment to do the right thing.
"He was on a yellow card and one more foul and all of the fans of Chelsea would be every time [trying] to pressure the referee to send him off.
"It was important to change."