Both City and Bayern have already qualified from Group D, and Pellegrini's team would need to beat the reigning European champions by six goals at the Allianz Arena to displace them at the top of the group.
With such scenario highly unlikely to happen, Pellegrini has hinted that his starting XI may be chosen with Saturday's Premier League clash with Arsenal in mind.
"Tomorrow we will see the XI that starts. Of course, it was one of the most important things to achieve - qualifying for the next round [already] and not deciding that here in Munich. So we will see tomorrow," Pellegrini told PA.
"Of course we are thinking about both things - firstly to do a very good game tomorrow, which is very important for us, and also what will happen in the tough game we have against Arsenal on Saturday."
City currently sit fourth in the Premier League table, six points behind league leaders Arsenal.