The French winger injured his ankle in Bayern's 7-0 thrashing of Shakhtar Dnestsk on March 11 and has not featured since.
Having returned to training over the international break, hopes had been raised that the 31-year-old may feature in the Klassiker.
However Bayern's left-winger will have to watch on from the sidelines, as will left-back David Alaba – ruled out for the majority of the rest of the season with a knee injury.
"This is not nice," captain Philipp Lahm told Bayern's official website.
"Although it does not help, we will not complain, we must just look forward.
"We have a large squad and must compensate for our losses."
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