Bayern Munich will meet Real Madrid, who beat holders Manchester City on penalties on Wednesday.
“They are fine and only went to hospital for a routine check-up,” said a spokesperson for the England captain.
The former Tottenham striker enjoyed a prolific record in north London derbies and a summer change of scenery made no difference.
The England captain is however no closer to that elusive first piece of silverware.
Kane is back in north London for the first time since leaving Tottenham last year as Bayern prepare for Tuesday's Champions League quarter-final first leg at Arsenal.
Saturday's "Der Klassiker" between Bayern Munich and Borussia Dortmund will unusually not be about controlling the title race or taking over the top spot in the German Bundesliga.
Brazil will hope not to break an ignominious 23-year-old record when they visit Wembley Stadium to square off against hosts England in a mouthwatering friendly on Saturday.
England captain Harry Kane will miss Saturday's friendly against Brazil and is "extremely doubtful" to face Belgium next week.
Harry Kane broke a 60-year record for most goals in a debut season while Jamal Musiala scored twice as Bayern Munich won 5-2 at Darmstadt on Saturday.
Kane is also the first English player to score 18 times in one season in the Bundesliga.
Bayern Munich striker Harry Kane said Robert Lewandowski's league goals record was "still a bit too far away" despite again scoring a brace in a 4-2 win over Heidenheim on Saturday.
The England striker slotted in from close range after nine minutes.
Bayern Munich striker Harry Kane joked that he would have to keep the match ball in his hotel room after scoring a Bundesliga hat-trick against Darmstadt on Saturday, as he is still yet to find a house in Munich.
Kane lobbed goalkeeper Marcel Schuhen from the centre circle to score Bayern's fifth and his second as Bayern tore Darmstadt apart on a rollercoaster afternoon for the champions.
Needing a point to be certain of qualifying for next year's tournament in Germany, Gareth Southgate's side fell behind to Gianluca Scamacca's early goal.
Harry Kane scored a second-half penalty as Bayern Munich claimed a 4-3 victory over Manchester United in their Champions League group-stage opener on Wednesday.
Bayern Munich striker Harry Kane said he "still had room to improve" after netting a fourth goal in four matches in his side's 2-2 home draw with Bayer Leverkusen on Friday.
Phil Foden and Harry Kane were also on target as the Three Lions tamed the roar of Hampden Park and Scotland's five-game winning streak on Tuesday.
Speaking after scoring twice on his home league debut in a 3-1 win over Bavarian derby rivals Augsburg, Kane said he was already building an on-field understanding with his colleagues.