But Germany goalkeeper Neuer, who has had foot surgery, and attacking midfielder Mueller, will be ready for next week's Champions League quarter-final first leg against Real Madrid.
The Bundesliga leaders, ten points clear at the top with seven matches left, face Dortmund again in the German Cup semi-final later this month.
Dortmund are in fourth place, 15 points behind Bayern and one behind third-placed Hoffenheim.
"We will not take any risk at this stage. But against Real they will both be ready," Ancelotti told reporters.
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Ancelotti will have winger Douglas Costa back against Dortmund after the Brazilian trained on Friday.
"He trained well and can play tomorrow," the Italian said.
"We will need our best team tomorrow. If we play well against Dortmund then obviously our confidence goes up ahead of the Real game. That's normal."
The Bavarians suffered their second league loss of the season when they were defeated 1-0 at Hoffenheim on Tuesday.
"We should not think too much about who we play against. We need to pay attention to our own quality."
(Reporting by Karolos Grohmann; Editing by Andrew Bolton)
