Just shy of the half-hour mark, the referee ordered both teams off the pitch after numerous balls were thrown on by fans, who were protesting against planned private investment in the Bundesliga.
Approximately five minutes later play resumed with the German champions 1-0 up thanks to Jamal Musiala's emphatic finish.
But a short time after play restarted Takuma Asano equalised for the home side.
Bochum then turned the game on its head on 43 minutes when Keven Schlotterbeck headed them in front in a first half which saw Kane miss a huge chance when Bayern were 1-0 up, while 14 minutes were added on at the end.
The match was then halted for a second time after the half time break with more tennis balls being thrown onto the pitch.
READ MORE ON HARRY KANE
Thomas Muller fumes at Harry Kane as Bayern Munich striker misses sitter
Tuchel admits Kane is 'not satisfied' at Bayern Munich and responds to 'leaked' rant
On this occasion the referee ordered both teams to come off the pitch and go down the tunnel while the pitch was cleared again.
Similar protests have been happening at other Bundesliga matches this weekend with chocolate and sweets among the objects also being thrown onto pitches.
Fans across the country have been unhappy for months over a planned sale of a stake in the Bundesliga's media rights company to an outside investor and have been protesting for weeks.
In four of five Saturday's matches protests interrupted play with the referees in both the Hoffenheim vs Union Berlin and Mainz vs Augsburg matches briefly sending the teams to the changing rooms.
Most read in Bundesliga
Tuchel admits Kane is 'not satisfied' at Bayern Munich and responds to 'leaked' rant
Thomas Tuchel's brutal seven-word rant at Kane and Bayern teammates after defeat leaked
Bayern Munich increasingly likely to sack Thomas Tuchel and it's bad news for Liverpool
Jordan: Kane won't be considered a failure even if he doesn't win any trophies at Bayern
Play resumed in both stadiums while the Wolfsburg vs Borussia Dortmund clash was repeatedly stopped to allow stadium staff to clear the pitch.
In December, Germany's first and second tier clubs voted in favour of letting a financial investor take a stake of the German Football League's (DFL) media arm in a deal estimated to be worth €900million and €1billion.
Raphael Honigstein reveals Thomas Tuchel and Harry Kane are under pressure at Bayern Munich following their Bundesliga loss to Bayer Leverkusen
Kane has enjoyed a stellar season for Bayern on a personal level but it's all going wrong for them in the title race.
A defeat will leave them with a mountain to climb in their quest for a 12th straight Bundesliga title as leaders Bayer Leverkusen's win at Heidenheim on Saturday left Bayern eight points adrift of the top prior to kick off at Bochum.