Robert Lewandowski scored twice after Arturo Vidal broke the deadlock in the first half, ensuring the champions moved six points clear at the top of the table, with second-place RB Leipzig drawing 2-2 with Bayer Leverkusen.
It was a particularly special win for Heynckes, who reached a half-century of wins in Germany's top flight from 1016 games, with 326 coming as a manager after 174 in his playing career.
500 - Jupp #Heynckes celebrates his 500th win in the #Bundesliga (174 wins as a player & 326 wins as a manager) - more BL wins than any other! Unique. @FCBayernEN @FCBayernUS #FCBFCA pic.twitter.com/fHSC0bZheO — OptaFranz (@OptaFranz) November 18, 2017
The 72-year-old, who replaced the sacked Carlo Ancelotti in September, is bidding to win his fourth Bundesliga title as Bayern boss this season, having previously guided them to glory in 1988-89, 1989-90 and 2012-13.