Costel Pantilimon continued in goal against Southampton on Saturday but the England No.1 will play in Tuesday's less consequential final Champions League group game
The England No.1 lost his place to Costel Pantilimon after a series of high-profile errors and, with a game against Premier League leaders Arsenal looming on December 14, the City boss intends to protect his current first-choice players in midweek.
"Joe Hart will play against Bayern Munich, sure," the Chilean, whose side are already guaranteed progression to the knockout stages, told reporters.
"Of course, if you ask me at this moment, the game against Arsenal next weekend is more important than the game against Bayern Munich.
"From the moment we qualified for the next round, the Premier League became more important than Champions League but that does not mean there is a possibility that the players who play against Bayern Munich will not play against Arsenal."
City were beaten at home by Pep Guardiola's side on October 2 but Pellegrini has no intention of changing his approach in order to compensate when they visit Germany.
"When you lose a game it is always for a lot of factors," he noted.
"This season we have played every game exactly the same. Against Bayern, was it because of the tactics? Maybe it was the players. Maybe they scored three goals that we should not have allowed.
"I will not change my tactics. Maybe because we are playing away, I do a different thing but, if I was to play that game again, I would do exactly the same."