Manager Roberto Mancini confirmed the Spaniard has not travelled to Germany with the rest of the squad for the final Group D match at the Westfalenstadion due to a hamstring injury.
City will now hope the 26-year-old can recover in time to feature in Sunday's eagerly anticipated top-of-the-table Premier League encounter with Manchester United.
Mancini said: "It's a hamstring. We don't know if he can recover for the derby. We will try."
City are also without midfield inspiration Yaya Toure, who is suspended for Tuesday's match against Dortmund.
Mancini's side are already eliminated from the Champions League and need to win in Germany to stand any chance of securing a consolation place in the Europa League.
There is a feeling City might be better served in their Premier League title defence by being out of Europe altogether but Mancini has disputed that.
The Italian also insists the upcoming derby against United has not clouded his thinking for the Dortmund game.
Mancini said on Monday: "We are a good team. We are a good club. We want to play well tomorrow and try to win.
"We have brought here all the players that are available. The other players that stay at home are injured. The players that are here will do everything to win this game.
"It will be difficult because I think in this moment Borussia are one of the best teams in Europe."