Neuer missed Bayern's 6-0 win over Augsburg at the weekend due to a foot injury, while Muller suffered an ankle problem in that game.
The duo will miss Tuesday's trip to Hoffenheim and could also be forced to watch Saturday's showdown with Borussia Dortmund from the stands, but Ancelotti has little doubt they will be available for the game against Madrid.
"Manuel starts training individually again on Monday," Ancelotti said at a news conference.
"He will 100 per cent certain play against Real Madrid.
"Muller needs a two-day break. We will see whether he can play against Dortmund. But we are convinced he will be ready for the game against Madrid. He does not have any pain.
"He did not train on Monday, but I expect him to return to the training pitch on Wednesday for some individual exercises.
"Douglas Costa's recovery is going according to plan. He resumes squad training on Wednesday.
"Thiago [Alcantara] will be rested on Tuesday. He has played a lot of games recently."