"At the start of the week all 23 players were healthy and available. But then Zanka got a muscle injury in training, so he will miss the game on Sunday," Wagner told a news conference.
"Jonathan Hogg is doubtful with a slight hip problem."
Wagner said Denmark international Jon Gorenc Stankovic would take Jorgensen's place in the team and hinted that they could also change their formation for the match against City.
"We have good players who are waiting for the chance to play. It's sad for us and Zanka but it's a big chance for other players," Wagner added.
"We'll work our socks off. There's no better occasion than Manchester City away. We'll be trying our best. We have to be confident. We know it'll be hard, but we'll stick together, be brave and fight."
Defending champions City began their campaign with a 2-0 win at Arsenal.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Christian Radnedge)
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