Jamie Gittens handed Dortmund the lead at the Signal Iduna Park with a powerful strike following a dazzling run down the left wing.
Matters were made worse for Bayern just moments later as their top scorer Kane went down onto the pitch holding his ankle.
The 31-year-old was swiftly substituted by manager Vincent Kompany in what could be a huge blow to the German giants.
Kane has struggled with ankle injuries throughout his career although has stayed relatively fit since signing for Bayern in 2023.
Thomas Muller was the man to replace him, with Bayern heading into half-time of the Bundesliga clash 1-0 down.
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Jamal Musiala equalised with five minutes left to play though as he headed in unmarked inside the box to seal a point.
Kane has scored scored 20 goals in 19 appearances for the club this season but it remains to be seen when he'll return to action.
Most of those have come in the Bundesliga and the England captain has also provided seven assists for his teammates.
The former Tottenham man's total league tally of 21 contributions is the most out of any player in Europe's top five divisions.
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He netted a hat-trick, his fourth of the campaign, in his previous Bundesliga outing for Bayern as they beat Augsburg 3-0 at home.
They are still yet to lose in the German top flight this season and held a six point lead at the top of the table heading into Saturday's match.
This has increased to seven, although Eintracht Frankfurt play their game in hand against Heidenheim on Sunday.
Dortmund last beat Bayern at home in 2018 when they won 3-2 but have claimed victory in just two matches since at all venues.
One of those came at the Allianz Arena last season to dent their opposition's title hopes heading into the crucial run-in.
They sit fifth in the table after 12 matches and are ten points behind Bayern following their second draw of the campaign.