The home side went into the game looking for a win that would keep alive their chances of topping the group.
Here, Sports Mole takes a closer look at the events that unfolded at the Etihad Stadium.
On Target 7
On Target 6
Was the result fair?
Despite the final scoreline, Manchester City can consider themselves fortunate to have won the game. Viktoria Plzen were expected to be comfortably beaten by the home side, but from the start they posed a real threat in attack. Their positive approach and desire was rewarded with two goals, but in the end their naivety at the back cost them, as City showed the power they possess in the final third.
Manchester City's performance
In the first half, City failed to produce any of the football that their home fans have been witnessing recently, with their first goal coming from a fortuitous penalty kick. In the second 45 minutes they were much more of a threat, with Jesus Navas and Yaya Toure making a real impact off the bench. They may have scored four goals tonight, but Manuel Pellegrini will be concerned at the way his team defended, with the second goal they gave away extremely poor for a team of their calibre.
Viktoria Plzen's performance
Viktoria Plzen had lost all of their group games before tonight and they would have been forgiven for trying to play for a draw, but their approach was refreshing. From the start they asked questions of the Manchester City defence and they responded brilliantly to twice come back from behind. Horava's goal was the best of the night and they will consider themselves unlucky to have left the Etihad Stadium empty handed.
Sports Mole's man of the match
Jesus Navas: Although Navas only came on at half time, the Spaniard was crucial to the home side's victory this evening. His forceful runs caused the opposition problems and opened up more space for City's attacking players. The winger set up two goals for his team, delivering inch-perfect crosses for Nasri and Negredo, showing just why his club paid big money for him this summer.
Toure may have helped swing the game in City's favour, but his manager will be disappointed that he picked up a yellow card that rules him out of their clash with Bayern Munich. The midfielder was booked for a poor tackle from behind in injury time that was completely unnecessary and gives his team even more of an uphill task at the Allianz Arena.
It was a relatively quiet evening for Firat Aydinus. The match official made the right call in awarding City a penalty for Frantisek Rajtoral's handball and he made no mistake with the yellow cards he handed out. The referee allowed the game to flow, which helped to produce an entertaining and very watchable encounter.
Manchester City: The Blues take on Swansea City in the Premier League on Sunday. Their next European fixture is on December 10, when they visit group leaders Bayern Munich.
Viktoria Plzen: Plzen host CSKA Moscow in their next Champions League game on December 10, where the two teams will fight for a place in the Europa League.