It was a very cagey opening with the match finely poised until Adam Isaacs opened the scoring for the Dons, reacting quickest in the box to turn home a Josh Cinna header on 22 minutes.
Isaacs was then in the right place at the right time again just four minutes later. This time, Cinna's long throw was flicked on by Zach Cohen, leaving Isaacs to tap in at the back post.
Not content with a two-goal margin at half-time, the Dons scored early in the second half. Another long throw was neatly headed home by Cohen in the 50th minute.
And Cohen made sure the game was out of sight for Bayern by the 67th minute, grabbing his second and the Dons' fourth of the day. He showed a superb turn of pace to chase down what looked like a lost cause and when he touched the ball past the Bayern keeper, he slotted in brilliantly from a seemingly impossible angle.
The Dons continued to look solid at the back and could easily have scored more before the final whistle.
Dons assistant manager Jamie Nagioff told JC Sport: "I think this was a defining moment in our season. Not just because we dominated against a title rival or because we now sit top of the league but because we showed a defensive maturity that I hadn't seen from us before.
"Until now, we hadn't kept a clean sheet this season, so to shut out the top side and top-scorer in the division shows just how good we were defensively.
"Harry Moss, in particular, was immense. Adam Ellis has tormented teams all season, including those in the Premier Division, but Harry ensured Ellis didn't get a look in today. The rest of the team were also exceptional defensively but Harry totally shut their main threat out the game.
"We knew we were in with a shout of going top because of our game in hand, but now we have the chance to pull five points clear of Bayern if we keep this momentum going over the next few weeks. It's an exciting time for the club right now."