The Chilean trainer explained that he had decided before the game to only give the Argentina international 45 minutes of action at the Etihad Stadium.
The Argentina international extended his remarkable start to the season by slotting home from the penalty spot at the Etihad to rack up his 15th goal in his last 12 appearances.
Aguero was replaced by Jesus Navas but Pellegrini revealed that it was always the plan to give the former Atletico Madrid man a rest ahead of Swansea City's visit on Sunday.
"He doesn't have any problems," the Chilean coach told reporters after the game. "He knew from the beginning he was just going to play 45 minutes."
Following Bayern Munich's 10th consecutive Champions League win against CSKA Moscow, it would take a 3-0 win in Germany for City to top Group D and Pellegrini says that overhauling last year's tournament winner is not the priority for his side.
"I think for the moment the Premier League [is more important]," he told Sky Sports. "We are going to play in Munich, we will try to win, but winning 3-0 in Bayern is not easy.
"It's important but more important is the next game [after that] when we play Arsenal."
The English side was twice pegged back by Plzen as first Tomas Hornava and then Stanislav Tecl breached its back line, and Pellegrini recognizes that his team's free-scoring nature must stall its defensive progress.
"Always when our team concede goals is a concern for me because we are not doing something well," he remarked.
"[On Wednesday] Plzen scored two goals and had two or three more chances. Last game, CSKA scored [twice]. It's important also to score but we must continue to improve."