The England international will replace Costel Pantilimon in goal as the Chilean is keen to keep his key players fit for Saturday's Premier League fixture at home to Arsenal
The top two in Group D meet at the Allianz Arena on Tuesday, having already reached the last 16, and City manager Manuel Pellegrini has confirmed that he will look to utilise some of his squad players with Saturday's clash with Premier League leaders Arsenal in mind.
"Joe Hart will play against Bayern Munich, sure," the Chilean confirmed after his side's 1-1 draw with Southampton on Saturday.
"Of course, if you ask me at this moment, the game against Arsenal next weekend is more important than the game against Bayern Munich.
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Bayern may also use the opportunity to rotate their squad as they look to extend their run of 11 straight wins in all competitions.
The reigning German and European champions demolished Werder Bremen 7-0 on Saturday to stretch their unbeaten Bundesliga streak to 40 matches, while Pep Guardiola's men set a new Champions League record of 10 consecutive victories when they won 3-1 at CSKA Moscow in November.
Bayern's last defeat in Europe came at home to English opposition when Arsenal won 2-0 in the second leg of their last-16 tie last season.
However, their last four Champions League games at the Allianz Arena have yielded four wins, with 14 goals scored and none conceded.
City have lost four of their eight away games in the Premier League this term, while Bayern have won 19 home fixtures in a row in all competitions since their loss to Arsenal.
Mario Gomez's double gave the Bavarians a comfortable 2-0 victory when they hosted City in the 2011-12 group stage, while Guardiola's men produced a masterclass to beat their opponents 3-1 at the Etihad Stadium on October 2.
Pellegrini only has injury concerns over forward Stevan Jovetic and defender Matija Nastasic (both calf) and will be without Yaya Toure as the Ivorian serves a one-match ban.
Arjen Robben (knee) is expected to be out of action for Bayern until the new year and he joins Holger Badstuber (knee) and Bastian Schweinsteiger (ankle) in being unavailable for Tuesday's fixture.