The Citizens travel to Germany on Tuesday to face the Champions League holders having already qualified for the knockout stages of the competition for the first time.
"Joe Hart will play against Bayern Munich, sure," manager Pellegrini 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."
Fit-again captain Vincent Kompany is one of those players likely to be rested after playing two games in the space of four days since returning from a thigh injury.