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.
Badstuber had recently returned from 20 months out with a double cruciate ligament injury and in his absence new signing Mehdi Benatia could make his debut on Wednesday in the home defence.
One bright spot for Bayern at the weekend was the return of Franck Ribery following a knee problem. The French midfielder made his first appearance of the season against Stuttgart, coming off the bench in the second half to score Bayern's second goal with five minutes remaining.
"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," Ribery said.
"But we're trying to make the best of it. We're doing everything we can so that we can still get results."
Ribery's decision to concentrate on club football was criticised last week by UEFA President Michel Platini, who suggested that the 31-year-old could be forced to serve a ban should he refuse a call-up to the France squad.
Ribery, who scored in Bayern's 3-1 win over City in Manchester last October, has dismissed his fellow countryman's comments.
"It doesn't really interest me," Ribery said. "I've decided to retire and people have to accept that."
Bayern captain Philipp Lahm also retired from international football this summer after leading Germany to World Cup glory. The 30-year-old is hungry for more success before his career ends though, particularly in the Champions League.
"I want to get my hands on the trophy again, whether it's this season or in the three years that follow," he told Kicker.
"With the squad we have at the moment, we have a chance to win the title."
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 ended Bayern's 10-game winning streak in the Champions League when they last met. But Alonso hopes his new club can get their revenge on Wednesday before facing other Group E opponents CSKA Moscow and Roma.
"Manchester City are among the 10 best teams in Europe," he said. "But we want to get the points."
Bayern manager Pep Guardiola and City boss Manuel Pellegrini know each other well from Spanish football. Ex-Barcelona coach Guardiola already faced the Chilean when he was in charge of Real Madrid, Villarreal and Malaga.
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," the Argentine defender said.
The Bayern defence should feature ex-City centre back Jerome Boateng.
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