The pair had tested positive for COVID-19 last week but both returned negative tests on Friday after their mandatory five day-isolation ended.
Germany international Muller, however, was still having some cold-like symptoms, Bayern coach Julian Nagelsmann said on Friday.
"Both are (COVID-19) free but Thomas still has some cold-like symptoms and he won't be in the squad. It is still too early for him to travel with us. He is not 100%," Nagelsmann told a news conference.
"Josh does not feel anything and all his values are high. We will wait for the last training and see what makes sense after five days. I assume he will travel with us."
Bayern are in third place in the Bundesliga on 15 points as many as fourth-placed Dortmund. Union Berlin and Freiburg lead the title race on 17.
Nagelsmann will also have France winger Kingsley Coman (26) back after a month out with a hamstring injury.
"He is fit and he overcame the stress tests. He is not a candidate to start... but he can play 30 or 40 minutes."
Both teams are going into Der Klassiker with midweek wins in the Champions League group stage. Bayern beat Viktoria Plzen 5-0 while Dortmund earned a 4-1 away win at Sevilla.
"Dortmund are a good team. They added some good players, lost some good ones too but they built a good team," Nagelsmann said.
"Especially when they defend deep and they can then hit you on the break. We saw that against Sevilla. They are playing a good season and it will be a good game. But what is important is that we are winners in the end," he added.
