Boss 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 Barclays Premier League encounter with United at the Etihad.
Mancini said: "It's a hamstring. We don't know if he can recover for the derby. We will try."
City tonight are also without midfield inspiration Yaya Toure, who is suspended for the match.
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 that City might be better served in their Premier League title defence by being out of Europe altogether now, but Mancini disputes that.
The Italian said: "We are a good team. We are a good club. We want to play well tonight and try to win.
"We have brought here all the players that are available. The other players that stay at home are injured. Those 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."