City manager Roberto Mancini has confirmed the Spaniard has not travelled to Germany with the rest of the squad for the final Group D match at the Westfalenstadion on Tuesday night due to a hamstring injury.
City will now hope the 26-year-old can recover in time to feature in this weekend's eagerly anticipated top-of-the-table Premier League encounter with United at the Etihad Stadium.
Mancini said: "It's a hamstring. We don't know if he can recover for the derby. We will try."
On Tuesday, City 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 has disputed that.
The Italian also insists the upcoming derby has not clouded his thinking for the Dortmund game.
Mancini said: "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."
Mancini knows the difficulties the Europa League can pose after his side also dropped into the second-tier competition last season.
But after being handed a tough Champions League group this season - with Real Madrid and Ajax making up the quartet - he is aware that progress could improve City's UEFA coefficient and help earn a better draw next time.
He said: "It could be difficult because in the Europa League you play Thursdays and you don't have a lot of days to recover for the Premier League, but we need to try to stay in the Europa League."
City have failed to win any of their first five Group D matches and are bottom of the pool with just three points.
To qualify for the Europa League and leapfrog Ajax they need to beat group winners Dortmund and hope Real Madrid, also through to the last 16, prevent the Dutch side winning in the Spanish capital.
City began the competition with much higher hopes and, given their resources, outside expectations were also greater but Mancini insists he is not embarrassed by the situation.
He said: "Embarrassment for what, I don't know, but we are disappointed because we wanted to go to the second stage this year.
"I think in football you need to learn. If there are other teams that play better than you and deserve to go through, we should accept this.
"If we didn't play well, Borussia and Real Madrid played better than us - we should accept this and we will try better next year."
Left-backs Gael Clichy and Aleksandar Kolarov are also out injured. Striker Edin Dzeko, who spoke alongside Mancini at a press conference at the stadium to preview the match, also has his sights set firmly on victory.
He said: "We still have a chance to play in the Europa League. We will do our best to try to win because only if we win can we continue in the Europa League.
"It won't be easy and we have a few players missing but we will do our best because everything is possible in football."
Dzeko is familiar with Dortmund having enjoyed a prolific spell in the Bundesliga with Wolfsburg before his £27million move to City two years ago.
The 26-year-old said: "They are a fantastic team, they have shown that in the Champions League.
"They have got a young team with some experienced players.
"I think we played good against Dortmund. I can't remember but I think I only lost one game against Dortmund.
"In the Champions League, we haven't played like we wanted and we only have two points but I think in the league we are playing very well. We haven't lost any games and I hope we will continue like that.
"In the Champions League there is one more game to play. We will try to win and if we can play in the Europa League that would be good for us."