The hosts, playing with 10 men, were unstoppable after the break against nine-man Darmstadt, opening their account with Kane's 52nd-minute diving header.
Leroy Sane struck twice, either side of a Jamal Musiala goal to kill off the game and Kane scored again with a stunning 60-yard looping shot from inside the Bayern half.
Thomas Muller added another and Musiala bagged his second five minutes later before ex-Tottenham man Kane completed his hat-trick with his 12th goal in nine league games.
D̴a̴̴v̴̴i̴̴d̴ ̴B̴̴e̴̴c̴̴k̴̴h̴a̴̴m̴, W̴a̴̴y̴̴n̴̴e̴ ̴R̴̴o̴̴o̴̴n̴̴e̴̴y̴, Harry Kane 🏴😱
A goal from the half-way line, UNBELIEVABLE! 🤩🔥 pic.twitter.com/Bmgk3FolpW
— Sky Sports Football (@SkyFootball) October 28, 2023
In a topsy-turvy first half, Bayern's Joshua Kimmich and two Darmstadt players were sent off with straight red cards, the first time this has happened in the opening 45 minutes of a Bundesliga game.
"That was a crazy first half against a tough opponent," Bayern coach Thomas Tuchel said.
"Overall, the first half had too many mistakes and we lacked intensity. After the break the response was clear. We had one extra player, we played out a lot of chances, scored a lot of goals."
"But it was an unusual game. No one expected it to end like this," Tuchel added.
Bayern are on 23 points, one ahead of Bayer Leverkusen, who play Freiburg on Sunday. VfB Stuttgart dropped to third place on 21 points following their 3-2 home loss to Hoffenheim.
RB Leipzig crushed Cologne 6-0 and are fourth on 20 points, level with Borussia Dortmund who can join Bayern at the top with victory over Eintracht Frankfurt on Sunday.
In Munich, all eyes were on the 37-year-old Manuel Neuer, who broke his leg in a skiing accident in December 2022 following Germany's early World Cup exit, and he received a loud welcome from the home fans as he led his team out as captain.
The celebrations, however, turned sour in the fourth minute when Neuer passed the ball to midfielder Kimmich, who failed to control the ball and pulled down Marwin Mehlem at the edge of the box to be sent off.
Even numbers were restored in the 21st minute when the visitors were also left with 10 men following the dismissal of Klaus Gjasula for a last-man foul on Konrad Laimer.
Neuer showed he was on track to get back to his very best when he stopped Mehlem's effort following a quick Darmstadt break before the visitors had another player sent off. Matej Maglica was ordered off in the 41st after bring down Kane, who was sprinting clear, setting a league record with three sendings-off in the first half.
There was no stopping Bayern after the break as they went on the rampage, scoring eight times in 37 minutes.
Darmstadt were helpless and Kane's audacious second goal was an early candidate for goal of the year.