İlkay Gündoğan's penalty is the difference between the sides at the interval.
Japan looked lively in the opening stages and had the ball in the back of the net, but Daizen Maeda's effort was ruled out for offside.
It was a clumsy foul from Japan goalkeeper Shuichi Gonda to concede the penalty after Japan had done well to keep Germany at bay for more than half an hour.
Kai Havertz then looked to have given Germany a 2-0 lead right on half time, but it was eventually ruled out by VAR for offside.
This game is far from over, with Japan still looking dangerous when going forward.