Ritsu Doan and Takuma Asano, both scored in the space of eight second-half minutes to put Hansi Flick’s side on the verge of elimination after just one game.
Germany had taken the lead in the first period, Manchester City’s Ilkay Gundogan coolly scoring from the penalty spot.
Japan found their rhythm when head coach Hajime Moriyasu freshened things up with a number of attacking changes which, ultimately, paid off as they brutally punished Flick’s side for their failure to convert in the final third.
Manuel Neuer had made one brilliant point-blank save to keep Germany in front, keeping out a deflected Junyo Ito effort, but when he denied Taki Minamino from close range, the ball fell kindly for Doan, who couldn’t miss from six yards in the 75th minute.
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And eight minutes later, Asano, too hot to handle down the Japan right for much of the match, fired a rocket into the roof of the net to secure a stunning comeback win for a side who managed just 26 percent possession.
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