The trio have excelled in what has ultimately been a disappointing season for Dortmund, who head into Der Klassiker in fourth place in the Bundesliga, 15 points behind Bayern.
In the last few years, Bayern have signed some of Dortmund's brightest stars with Mario Gotze, Robert Lewandowski and Mats Hummels all moving to the Bavarians.
The win restored Bayern's 10-point lead at the summit following RB Leipzig's victory over Bayer Leverkusen earlier on Saturday with just six rounds remaining.
Mueller and Neuer are being rested to be sure of playing in Bayern's Champions League match with Real Madrid on Wednesday.
"It's too soon for Manuel Neuer - we don't want to take any risks", Ancelotti told a news conference.
The hosts, though, never stopped charging forward and Arjen Robben was denied four times in the first half with his trademark move, cutting in from the right.
Dortmund are chasing a second win over Carlo Ancelotti's Bayern this season after sealing a 1-0 victory over the Bavarians last November when Aubameyang hit the victor.
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Lewandowski scored with a free kick and a penalty to take his tally to a Bundesliga-leading 25 goals, overtaking Dortmund counterpart Pierre-Emerick Aubameyang.
"I'd have been surprised at anything other than this dominance and this result", Tuchel said in his press conference, according to their opponents' official website. He showed a constant threat down the right wing and showed why despite being 34, he remains a first-choice player in the biggest matches for Bayern. "But we're anxious about how we get him back. It's a bitter experience".
Quickfire goals from the recalled Franck Ribery and Robert Lewandowski saw the home side race into a 2-0 lead inside 10 minutes before a stunning Raphael Guerreiro strike halved the deficit.
If Bayern can repeat one of their recent performances at the Allianz Arena, they'll go past Dortmund's 1.5 goals conceded per match average in away matches.
BBC reports that Carlos Ancelotti's side look unstoppable as they close in on a record 27th German title and still have a unique European and domestic treble in their sights.
"It will be a tough task. We did get back into it, but conceding the third directly after the interval put the game beyond us".