Germany, third at the last worlds, were outgunned by Japan, whose young charges fought back from one match down to stun the Europeans 3-1.
Teenage star Jun Mizutani said Japan had been relishing the chance to take on Germany, who are competing here without their champion, injured world number five Timo Boll.
"We have been training specifically to play Germany," said Mizutani who lost his first encounter before firing back to clinch the fourth for Japan.
"I was nervous during my first game, I made mistakes and played badly but in the fourth game I had so many tactics going around my head," Mizutani, 18 said.
German coach Richard Prause denied that Boll's absence caused their defeat, crediting Japan for being more aggressive than his team.
The win pushes Japan, 14th at the last championships, to the top of their group with one round of matches left to play before the finals kick off at the Guangzhou Gymnasium.
In other games, China's men took just under an hour to dispose of Austria, the Red Army using the encounter to hone their formidable skills ahead of the Olympics on home turf later this year.