Scorers: Manchester City - Aguero (33 pen), Nasri (65), Negredo (78), Dzeko (89); Viktoria Plzen - Horava (43), Tecl (69)
With a place in the last 16 already secured, City were below par at the Etihad Stadium and were twice pegged back by the Czech minnows before seeing out the victory late on.
Sergio Aguero and Samir Nasri both put Manuel Pellegrini’s men ahead but Tomas Horava and Stanislav Tecl responded, before Negredo and Dzeko finally clinched victory in the last 12 minutes.
Pellegrini had made seven changes for the match – including restoring England goalkeeper Joe Hart – but it needed the late introduction of Negredo to finally tilt the game their way.
Dzeko, who had laboured for little reward, put the game beyond doubt in the last minute, setting up a potential group decider with Bayern Munich next month.
The victory was all that City required but the performance of some of the players brought in, and the defence in general, will be a cause for concern for Pellegrini.
City started brightly before some all-too-familiar sloppiness at the back, in the continued absence of captain Vincent Kompany, allowed Plzen to grow in confidence. But on the issue of Hart’s return, after five games on the bench, the goalkeeper could at least be pleased with his efforts after making a couple of good flying saves.
The result kept City three points behind Bayern Munich, who had earlier enjoyed a record tenth straight Champions League win in Russia, ahead of their meeting in Germany in two weeks.
Manchester City: Hart, Richards, Demichelis, Lescott, Kolarov, Milner, Javi Garcia, Fernandinho (Toure 64), Nasri (Negredo 75), Aguero (Jesus Navas 46), Dzeko. Subs not used: Pantilimon, Zabaleta, Boyata, Huws.
Viktoria Plzen: Kozacik, Rajtoral, Cisovsky, Prochazka, Hubnik, Petrzela (Kovarik 73), Horava, Horvath, Duris (Wagner 89), Kolar (Bakos 85), Tecl. Subs not used: Bolek, Hejda, Reznik, Pospisil.
Referee: F Aydinus (Turkey)