The referee halted the game 38 minutes into the second half due to the lightning, and the game was scrapped seven minutes later.
The only goal came in the 68th minute soon after the visitors faced a scare when midfielder Yohei Kajiyama's shot was saved by Argentine goalkeeper Oscar Ustari. Argentina counter-attacked, with Sergio Aguero speedily moving up the centre to send the ball to fellow forward Angel Di Maria in the front line, who fired home from the edge of the box.
Japan fought throughout the match. Midfielder Keisuke Honda's middle shot hit the bar in the 58th minute, while Honda created Japan's best chance on a free kick in the 10th minute - though Masato Morishige's shot was saved by Ustari.
"I have mixed feelings, I can't help it," said Japan coach Yasuharu Sorimachi. "Our real competition starts in Beijing. We are going to prepare for it from now on."