Bundesliga top-scorer Mario Mandzukic headed them in front just before the break with Bastian Schweinsteiger sealing victory shortly after the interval.
Stefan Kiessling nodded in a consolation in stoppage time to make the final score 2-1.
With Borussia Dortmund losing earlier on Saturday, Bayern now have a 23-point advantage at the top of the table and could wrap up the title quicker than anybody ever before with a win at Mainz next weekend.
Leverkusen, who drew at home to Bayern earlier this season, were the last side to beat the Bavarians in October 2012.
They showed why they have proven to be a thorn in Bayern's side with a bold beginning to the game, Stefan Kiessling sending Heung-Min Son through for a good early chance which the South Korean slotted wide of the far post.
Kiessling was almost faced with only Manuel Neuer to beat in the 14th minute, but the offside flag stopped him in his tracks.
While they were not creating many chances, Bayern were playing their usual possession game and they finally made the breakthrough just a minute before half-time.
Schweinsteiger lifted a ball into the area and Mandzukic showed why he's the Bundesliga's top marksman with a determined leap and header past Bernd Leno from close range.
The contest was effectively over seven minutes into the second half when Schweinsteiger curled in a direct free-kick which grazed the underside of the crossbar on its way past Leno.
Simon Rolfes flashed a volley over the crossbar, but Bayern's lead was never in any doubt.
Coach Pep Guardiola was able to rotate his players around again with Arjen Robben removed for a rest, but still they looked invincible, even if Kiessling headed in a late consolation.
Even in their first match since Uli Hoeness resigned as president after being sentenced to prison for tax evasion, Bayern showed they are in a league of their own as they edge closer to winning the title in record-breaking time - as early as next Saturday, with nine league games of the season still to go.