The 31-year-old led the line for his side's 1-1 stalemate with the reigning German champions, where an Aleksandar Pavlovic rocket cancelled out a 31st-minute strike from Robert Andrich.
For the first time in the 2024-25 Bundesliga season, Kane failed to register a goal or assist in a game, and the England captain's evening ended slightly prematurely as he was forced off in the 86th minute.
Kane had gone down in agony following a challenge from Leverkusen's Amine Adli, and he was evidently furious about the incident before being replaced by Thomas Muller for the final exchanges.
Kane's scare has certainly come at a less-than-ideal time for club and country, as Bayern Munich will head to England on Wednesday evening for an intriguing Champions League contest with Aston Villa.
Kane, Vincent Kompany share update on striker's injury
The next international break is also imminent, as the Three Lions endeavour to continue their positive start to life under Lee Carsley against Greece and Finland in the UEFA Nations League on October 10 and 13 respectively.
Bayern boss Kompany was keeping his fingers crossed that Kane would be fine for the midweek trip to Villa, though, telling Sky Deutschland: "I'm not a doctor, but I hope that maybe it will be enough for Wednesday."
Kane also played down the severity of his incident after the match, although he was bewildered that the challenge from Adli did not even warrant a booking, claiming that a red card could have been a suitable punishment.
"It was really painful at first and it was annoying to miss the last five or ten minutes of the game. Sometimes there have been red cards for something like that," the former Tottenham Hotspur man said.
Bayern CEO Jan-Christian Dreesen also made a reassuring statement at full time, saying: "He took a hit. But as the doctors said, it's probably nothing serious. We'll have to look at it again tomorrow."
Who could replace Kane for Villa, England games?
While Kane will require more tests to determine the severity of his problem, the initial signs appear to be promising for the England skipper, who has already registered 10 goals and five assists in just seven appearances this term.
However, should the striker's problem prove more serious than first feared, Kompany could be forced to shoe-horn Muller or Mathys Tel into a central role for the trip to Villa, whose own marksman could deputise for his senior in the national team.
Indeed, Ollie Watkins is currently Kane's England backup but should be the first port of call if Spurs' all-time leading scorer is not passed fit, although Ivan Toney is still being watched by Carsley.
The Al-Ahli man did not make September's squad after a hectic summer transfer window, but Carsley has insisted that he remains under consideration for future selections.