Joe Hart made a blemish-free first club appearance for a month and Manchester City can still win Group D although that will be difficult given the final game is at the home of the European Cup holders, Bayern Munich.

Each of these headlines should please Manuel Pellegrini, but City's slipshod defending and application is less palatable to a manager who demands consistent high performance. Until Alvaro Negredo tapped in 12 minutes from time and Edin Dzeko's late header confirmed the win, Viktoria Plzen were heading for a first point of the phase which, given City's superior quality, was hardly desired.

Despite fielding a B-list defence featuring Hart, Micah Richards, Martin Demichelis, Joleon Lescott and Aleksandar Kolarov, Pellegrini pointed at deficiencies in the whole side. "One of the most important things to be an attacking team is to know how to defend well," he said. "Today we did very, very bad. I am satisfied because we won the game 4-2, but I think we didn't play well – we didn't play with the intensity and the pace we are playing at home.

"I am not talking about just Richards and Lescott, I am talking about the whole team. 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."

There were kinder words for his goalkeeper. "I think Joe Hart played very well. 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," the manager said.

Pellegrini was not prepared to say if Hart had done enough to start against Swansea City here on Sunday. "From tomorrow we will start thinking about the next game. Now we are talking about the Premier League."

Pressed again if the thinking is that Costel Pantilimon remains in his strongest side until the Romanian's form dips, Pellegrini did offer Hart a glimmer of hope. "I repeat, today I am thinking about Champions League. From tomorrow, we will start thinking about who is the best 11 to start for the next game, from the goalkeeper to the other players," he said.

Hart had been given the nod by Pellegrini in an XI containing only three first-choice players – Fernandinho, Sergio Agüero and Samir Nasri – with the rest second-stringers, a category into which the England goalkeeper has fallen.

When the Plzen captain, Pavel Horvarth, swung in a free-kick from the right it went straight at Hart for him to collect. This was the sum of all questions posed to Hart until the 24th minute, when another aerial delivery was once again taken smoothly.

Then he released Agüero quickly with a punt downfield from which the striker might have given City the lead. Instead Firat Aydinus, the referee, wrongly whistled for an infringement on the edge of the area and though Agüero went on to finish, it counted for nothing.

Hart should then have had to pick the ball out from his goal twice. He could do nothing when Frantisek Rajtoral was allowed to slip through unchallenged before fashioning an effort that if either a decisive shot or pass should have given Plzen the opener. Instead, the ball rolled harmlessly wide of Hart's right-hand post. There was an even clearer chance when Daniel Kolar left Lescott behind and squared to Michal Duris, but his glancing effort was misdirected.

Moments later, Rajtoral was adjudged to have handled in the area and the referee pointed to the spot. Agüero, on 15 goals in 15 appearances this season beforehand, duly maintained his goal-a-game ratio, giving Matus Kozacik no chance.

Yet as half-time beckoned Plzen shocked City, scant resistance from the midfield allowing Tomas Horava to collect and beat Hart with a piledriver shot to his right.

Agüero's removal for Jesús Navas at half-time proved a precaution – "Sergio hasn't any problems. He knew from the beginning that he was going to play just 45 minutes," Pellegrini confirmed – before the excellent Nasri appeared to have won the game for City by finishing from close range for his third of the season.

But a mix-up in the home area reminiscent of the away form that has handed City four losses in their last six league outings allowed Stanislav Tecl to score Plzen's second goal.

If Negredo and Dzeko had not intervened, Pellegrini would have been even more unhappy. As it was he was left a relieved man who could afford to praise the opposition. "Yes, they played very well. It is a merit of Plzen the way they play. I saw the last game they played against Bayern Munich, I thought they did really well," he said. "I talked to the players before and said if you give them space and time they will do damage."