Ralph Hasenhüttl's charges had lost all four of their previous encounters with the record Bundesliga champions and looked to be on course for a fifth defeat after falling behind to Sandro Wagner's 12th-minute header.
However, Liverpool-bound Keita turned on the style in midfield and scored a deserved equaliser shortly before half-time. He collected the ball from full-back Konrad Laimer in the corner of the box and smashed home into the top corner beyond Sven Ulreich at the second time of asking.
Indeed, it was a hugely impressive performance from the hosts – and Keita in particular – with the 23-year-old's goal coming from Leipzig's 11th shot in the first 45 minutes. To put that into context, Bayern had not allowed any opponent to have as many efforts during a first half all season.
The Guinea international was outstanding after the interval too, setting up Timo Werner to score the winner in the 56th minute with a perfectly weighted pass. Leipzig's 2-1 victory means they have won all 11 Bundesliga games in which Keita has found the net, once again affirming his importance to the side.
Couple his goal and assist with a first ever win over the record Bundesliga champions, and Naby Keita is a worthy winner of this week's Man of the Matchday honour.