The opening game in Group E on Wednesday sees the German and English champions meet in Munich's Allianz Arena, where City came back from two goals down to win 3-2 in their final group game last December.
While City went on to lose to Barcelona in the last 16, group winners Bayern were hammered 5-0 over two legs by eventual winners Real Madrid in the semi-finals.
Bayern sit joint top of the Bundesliga after three matches, but they have a lengthy injury list going into their first European match. Midfielders Bastian Schweinsteiger, Javi Martinez and Thiago are all out with knee injuries and the Bavarians suffered another blow on Saturday when Holger Badstuber limped off with a thigh injury in the 2-0 win over VfB Stuttgart.
One bright spot for Bayern at the weekend was the return of Franck Ribery following a knee problem.
"We're currently in a very difficult situation at the moment because we have a lot of players injured and players who are not yet fully fit,” said Ribery.
"But we're trying to make the best of it. We're doing everything we can so that we can still get results."
Two-time Champions League winner Xabi Alonso is set to make his first appearance for Bayern in the competition since his move from Real Madrid.
City Manuel Pellegrini will serve a touchline ban on Wednesday, while he will also be without Argentine full-back Pablo Zabaleta after he was sent off against Barcelona last season.
Martin Demichelis, who scored City's late equaliser in a 2-2 draw with Arsenal on Saturday, returns to his former club.
"It will be extremely emotional for me because Bayern were the club that gave me the chance to come to Europe and play," said the Argentine defender.
Cesc is Fab for Costa, says Mourinho
Chelsea’s Diego Costa and Cesc Fabregas will take their promising partnership into Europe for the first time on Wednesday when the Blues host Schalke in their opening Champions League Group G fixture and Mourinho expects Costa to benefit from more Fabregas magic against the German club.
Costa has adapted seamlessly to life in the Premier League following his £32 million move from Atletico Madrid in the close-season and the Spain international took his goal tally to seven from just four matches with a hat-trick in Chelsea's 4-2 win over Swansea on Saturday.
Blues boss Mourinho is delighted with Costa's predatory finishing and combative style, but he believes the probing passes of Spain midfielder Fabregas have been just as instrumental in the Brazil-born star's success.
"To play with Fabregas is the dream of every striker," Mourinho told Chelsea TV.
"The guy sees the movement, sees the pass, is not selfish and always makes the right choice."
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