Plzen twice pegged City back with Tomas Horava and Stanislav Tecl replying to Sergio Aguero's penalty and Samir Nasri's goal.
Late efforts from Alvaro Negredo and Edin Dzeko won the day for City, but Pellegrini was not too happy with the performance.
"I think we didn't play well," he told Sky Sports.
"Of all the matches we have played in the Premier League, Champions League, Capital One, all the games we have played Joe Hart has had the most work in the match, they had a lot of chances, they played well, but finally we won."
City made seven changes to their side for the match, but Pellegrini insisted that was not a mistake.
"I think we made the changes we had to," he said.
"We had already qualified for the next stage and Bayern had won against CSKA so it is very difficult for us to be first in the group, we are going to try but it is very difficult. We have to win 3-0 in Munich and after that game we have to play against Arsenal."
Pellegrini feels that Plzen had more 'motivation' for the game, adding: "Motivation is very important and Plzen had that, as they fight for the Europa League and that was the difference, the intensity they put into it."
Whilst City are keen to secure top spot with victory over Bayern, Pellegrini admits the Premier League is now their main concern.
"I think for the moment, the most important thing for us is the Premier League," he said.
"We will go to Munich and try and win but winning there is not easy, it is important but more important is the game after that with Arsenal."
The City boss admits he is not happy with the amount of goals his team have been conceding in recent games.
"When our team concedes goals it is always a concern as it is something we are not doing well," he said.
"They scored and had two or three more chances and the last game with CSKA too, but we must continue improving in that sense."
The Chilean believes that City could be left with a tough draw as they look set to finish in second.
"We must wait for the draw in December, sure it will be tougher against a Spanish team or PSG - we must see who finishes in first in other groups but I have a lot of trust in this team," he added.
On Hart and his return to the team he refused to be drawn on whether he could be recalled for Premier League games too.
"He did very well, we will see - we are talking about Champions League, not Premier League yet," he said.
He also confirmed Sergio Aguero was not injured despite going off at half-time.
"Sergio we made a change as he is playing too much and from the beginning he knew he was only playing 45-minutes," he said.