Aguero opened the scoring from the penalty spot in City's 4-2 UEFA Champions League victory over the Czech club on Wednesday, but was replaced for the second 45 minutes by Jesus Navas.
And manager Pellegrini revealed the 25-year-old striker was only ever going to play the first half.
"Aguero hasn't any problems," he said. "He knew from the beginning he was just going to play 45 minutes."
Joe Hart also made his return to first-team action against Plzen, having not featured since the end of October, but Pellegrini refused to be drawn on whether the England goalkeeper would remain in the side for Sunday's Premier League clash against Swansea City.
"I think Joe Hart played very well," he continued.
"I didn’t expect that he would have to work so much during the game because I think this is the match when the other team, including Champions League and Premier League, had the most chances to score.
"Now we are talking about the Premier League. I repeat, I think Joe did a very good performance."
City are already through to the last 16 and sit three points behind Group D leaders and defending champions Bayern Munich with one match - against the Germans - left to play.
