Australia defender Aziz Bahish netted the ball in the 85th minute on Tuesday to give Japan a 2-1 win and six points from four matches in Group B, three ahead of the Australian first.
Australia goalkeeper Matt Ryan fired a shot from Takuma Asano and the ball bounced off the post and then bounced off Bahich and into the net.
Ao Tanaka gave Japan an early lead at Saitama, but Agden Hrucic equalized for Australia in the 70th minute.
Australia, who have won 11 games in a row, were awarded a penalty midway through the second half when Hidemasa Morita knocked out Hrostik on the edge of the area.
Japan are seeking their seventh consecutive World Cup appearance. Australia has appeared in every World Cup final since 2006.
Son Heung-min gave South Korea the lead at the start of the second half. Alireza Jahanbakhsh then scored the equalizer to keep Iran at the top of the group with 10 points, two points ahead of second-placed South Korea.
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