Goals from Franck Ribery, Arjen Robben and Thomas Muller did the damage on a chastening night for the Blues.
However, the 60-year old repeatedly refused to pick out and criticize individuals for the defeat in his post-match press conference.
“I will talk about the team not individuals,” Pellegrini declared.
“We played really bad today – it’s not the team we’ve seen every week in the Premier League and I think that was the worst thing.
“We didn’t have possession and we didn’t do enough to have more. Of course Bayern always have a lot of the ball but today wasn’t a good day for us.
“It’s your duty as journalists to analyse individual players, I think we didn’t play well but of course we could do better on the goals, not only the goalkeeper.
“You can concede goals against Bayern Munich though because they’re a very good team.
“The difference between City and Bayern Munich may not be what we saw today. There are a lot of reasons why this happened today and it’s important for me to find solutions to that.
...Manuel Pellegrini...
“It’s just one game, you can have a lot of conclusions from just one game but of course we can improve a lot – we have the quality to qualify for the round of 16.”
The introduction of goalscorer Alvaro Negredo, as well as the entrances of David Silva and James Milner seemed to shift the game in City’s favour.
But the City boss believes that the game was well over by the time the trio were on the pitch.
“I think the three substitutes did very well and we changed a little more than that. In the last 15/20 minutes we were better,” the boss stated.
“It’s an important thing about the squad we have but it wasn’t enough to change the result – from the start we were OK but once they scored, we were losing the ball and that’s very dangerous against this Bayern team.
“I was surprised by the game we played today – the goal Negredo scored was just a little thing at the end.
“I think that me and all of the players know exactly what we must do to do well in the Champions League going forward.”
One rare bright spot for Manuel on the night was the re-emergence of Micah Richards.
The 25-year old has not played a lot of football in the last year but Pellegrini believes that the right-back played very well against one of the world’s best wingers in Franck Ribery.
“I think Micah Richards played very well in the game, Ribery is a very dangerous winger and I don’t think that Ribery was the key factor to win the game today, so I don’t think Micah has responsibility for the score.
...Manuel Pellegrini...
“I don’t think he had a special problem on that side.”
Pellegrini’s Bayern counterpart Pep Guardiola admitted that it was the best performance he had seen in his short reign as Head Coach of the European champions but believes that City will still qualify with his team from Group D.
“I’m very happy with our performance – we’ve got six points which is a good step towards qualifying for the next stage,” Guardiola asserted.
“We dominated the game and possession, we switched play and won the ball back very well. I’m very, very happy.
“I have a lot of respect for Manuel and his players – I said yesterday, and nothing changes my mind from tonight – I said I think City will qualify and they will be a tough opponent in the next round for whoever draws them.
“It’s not an easy game when you play against City with their unbelievable players.
...Pep Guardiola...
“Football is special - when David Silva hit the crossbar with his free-kick late on, I thought, anything could happen if it goes in.
“Today we are so happy with our performance in a country that loves football.”
