Muller provided the assist for Robert Lewandowski's opening goal, before scoring himself to give Bayern a 3-0 lead after 23 minutes. It was 5-0 by half time, with Lewandowski completing a hat trick late in the second half to compound Dortmund's misery.
Muller's goal was significant because it elevated him to fourth in Bayern's all-time list of Bundesliga scorers, passing Dieter Hoeness' tally of 102.
Muller's next target is Roland Wohlfarth's 119 Bundesliga goals, followed by Karl-Heinz Rummenigge, who scored 162. Gerd Muller's remarkable club record of 365 league goals is unlikely to ever be surpassed.
Schalke's 2-0 win over Freiburg on Friday meant that Bayern could not have sealed the title in Der Klassiker, but they are now just one win away from clinching their sixth consecutive Bundesliga crown.
Jupp Heynckes' team now travel to Augsburg next Saturday knowing that a win would be enough to give them their first major honour this season.
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Heynckes is looking to replicate the treble that he guided Bayern to in 2012-13, when they won the Bundesliga, DFB-Pokal and Champions League in the same season.
Bayern face Sevilla on Tuesday in the first leg of their Champions League quarter final, and will play Bayer Leverkusen in the DFB-Pokal semi final later this month.
Muller scored his first Bayern goal against Sporting Lisbon in the Champions League in 2009, and has consistently chipped in with goals ever since. His most prolific season was 2015-16, when he scored 32 times in all competitions.