In what Bayern boss Daniel Holder described as the division's "biggest game of the season," Bayern started the game fairly brightly, with their best chance falling to Eli Davila from a set-piece but his effort was blocked.
Adam Biton then saved Bayern as a set-piece fell to a Dons player two yards out before an incredible goal line cross somehow kept the ball from going in.
The Dons forged ahead midway through the first half as an excellent down the right flank found their winger who crossed for Zack Cohen to tap home. The hosts had more chances to double their advantage but Bayern, inspired by goalkeeper Joe Nyman, kept them at bay.
Half-time came and Bayern we confident they were "more than capable of turning it round". But it was the Dons who came close in the opening stages of the second half from another set-piece.
Bayern drew level in the 65th minute with their first decent passing move which saw the substitute Nicky Cooper find Davila who played in the returning skipper Jake Dayan. He fired goalwards from 25 yards, the ball was parried into the path of left-back Cooper who finished for his first goal in a Mincha shirt.
The Dons were panicking after the goal and more gaps were finally opening. Just 10 minutes later referee Darryl Colmans whistled following a handball in the area and Bayern talisman Ellis coolly slotted home the resultant penalty, sending the keeper the wrong way as the celebrations erupted.
Bayern were then reduced to 10 men as Adam Biton was sent off following a sliding challenge. The Bayern managment described the decision as "very harsh" and "hope this can be reviewed on When Sunday Comes, so it gets overturned".
The visitors reveted to five in the middle to see out the last 10 minutes and they were relieved to hear the final whistle as they put daylight between themselves and the Dons.
Bayern joint-manager Daniel Holder told JC Sport: "It certainly wasn’t our best performance of the season but we ground out the result and that’s all that mattered.
"This could be an instrumental moment in the season as it puts us top, but we still have seven cup finals left to play.
"We got outplayed by Dons just a few weeks ago as we lost 4-0, but with five wins on the bounce since the break, it shows how far we’ve come."
Dons boss Brandon Hamme told JC Sport: "We looked control in the first half but in the second half we were second best and struggled to create anything, was a tale of two halves and our inability to finish our chances in the first half came back to bite.
"The goals we conceded were unfortunate but Bayern were class today and they deserved the win. They will be pushing us until the very end for promotion, we know we are in for a fight.”