After netting a brace against Shakhtar Donetsk in midweek, a confident Michael Olise threatened to grab an early opener when he fired a left-foot shot against the outside of Robin Zentner’s right post.
But Mainz weren’t daunted and soon offered their own threat through Jonathan Burkardt, who injured himself in the process of firing just wide of Daniel Peretz’s goal.
The hosts didn’t look back from there and continued to make promising inroads while also preventing Bayern from building any sort of momentum.
And ‘promising’ then became ‘meaningful’, as Mainz’s Lee broke the deadlock just before the interval, guiding the ball home from Armindo Sieb’s deflected cross, after Kim Min-Jae and Olise failed to deal with a cross-field ball, ensuring the hosts took a surprise lead into the break.
There had been plenty of encouraging signs for the hosts overall, but with their opponents having netted an incredible 28 times across the previous six meetings, this was far from over - especially against a Bayern side that was yet to trail by two goals in the Bundesliga this season.
But after an assertive start to the second half from Mainz, that statistic soon changed when the Lee and Sieb double act provided a second goal on the hour mark.
The South Korea international collected Sieb’s low cross from the right flank before he swivelled and fired past Peretz - with the aid of a slight deflection off Joshua Kimmich - to leave the home supporters in dreamland.
Lee’s fifth league goal of the season knocked the stuffing out of Vincent Kompany’s side, who looked far from a team that had racked up 41 goals in their previous 13 league matches.
Bayern eventually showed signs of life when Leroy Sane pulled a goal back in the 87th minute, tapping in from Kimmich’s deflected effort.
However, it was ultimately too little too late, as Mainz held their nerve to see out the closing stages, clinching a third consecutive home win and duly climbing up to sixth spot.
On the flip side, Bayern’s lead at the top has reduced to four points, following Kompany’s first Bundesliga defeat.
Flashscore Man of the Match: Lee Jae-Sung (Mainz)