A goal in either half has seen Japan edge out the Caltex Socceroos 2-0 in their FIFA World Cup qualifier in Saitama on Tuesday night.
Ange Postecoglou’s side enjoyed long periods of possession throughout the match but were unable to make it count against the Samurai Blue.
Takuma Asano and Yosuke Ideguchi scored the goals for the hosts as they guaranteed their spot at next year’s World Cup in Russia.
The Caltex Socceroos were without star midfielder Aaron Mooy through illness, while Tomi Juric could only start on the bench due to an injury which kept him from training all week.
After an even start, Mathew Leckie came within inches of the opener, controlling Massimo Luongo's lay-off before sending a deflected effort off the base of the left-hand post from the edge of the area.
Then five minutes before the break Asano broke the deadlock after Nagatomo clipped a fine delivery in from the left and the Japanese winger side-footed a simple volley past Mat Ryan.
Postecoglou introduced Juric in the second half as they began to push for a way back into the contest, while fellow substitute Tim Cahill came within inches of meeting a Robbie Kruse cut-back at the far post.
Trent Sainsbury made a brilliant goal-line block to deny Ideguchi a second but it proved in vain for Australia, as the 21-year-old cut inside from the left before rifling an unstoppable shot past Ryan and into the top corner from 20 yards out in the closing minutes.