City were twice pegged back by the Czech minnows at the Etihad Stadium before late goals from Alvaro Negredo and Edin Dzeko secured a 4-2 win in the Group D encounter.
Sergio Aguero, from a penalty, and Samir Nasri had both put City ahead but Plzen responded each time through Tomas Horava and Stanislav Tecl.
Goals have not been a problem for City - with 22 now scored in the last four home games - but questions continue to recur about the defence, particularly in the continued absence of captain Vincent Kompany.
Pellegrini said: "We can attack and we can score four goals, but without giving (away) as many chances as we did today in defending.
"One of the most important things to be an attacking team is to know how to defend well. Today we did very, very bad.
"I am talking about the whole team. I think the whole team must know how to defend.
"We didn't have the intensity or the pace today to do it and I am not talking about individual players."
Little blame for City's defensive shortcomings could be directed at goalkeeper Joe Hart, who was restored after five games on the bench.
The England international made some good saves and Pellegrini was pleased with his performance, although he would not confirm whether he or Costel Pantilimon would face Swansea at the weekend.
Pellegrini said: "I think Joe Hart played very well.
"I didn't expect that he would have to work so much during the game but I think this is the match when the other team - including Champions League and Premier League (games) - had the most chances to score.
"From tomorrow we will start thinking about the next game. Now we are talking about the Premier League but, I repeat, I think Joe had a very good performance."
Plzen, with a Europa League place still to play for, put up much more of a fight than when they were beaten 3-0 by City in September or lost 5-0 to Bayern Munich.
City, who are already through and made seven changes, were below par but they still have a chance to overhaul Bayern at the top of the group - if they beat the Germans at least 3-0 next month.
Pellegrini said: "I am satisfied because we won the game 4-2 but I don't think we played well, we didn't play with the intensity and the pace we are playing (with) here at home."
Top scorer Aguero, who has now scored 15 in his last 12 appearances, was taken off at half-time but Pellegrini said there was no injury.
He said: "Sergio hasn't (got) any problems. He knew from the beginning that he was just going to play just 45 minutes."