The German international broke a bone in his foot in April, and the start of the Bundesliga has come to soon for him.
'Manuel Neuer will not be playing on Friday. We will not take any risk', Ancelotti said to reporters.
There is a very long injury list at Bayern, including Jerome Boateng, Thiago, Javi Martinez and new signing James Rodriguez.
However, the Italian manager will have David Alaba and Arjen Robben back as both have successfully recovered from their injuries.