Everton midfielder Tim Cahill was the hero with two late goals as he dragged Australia’s campaign back from the brink before Alaves striker John Aloisi rounded out the scoring in injury time.
Japan went ahead in the first half through a contentious goal to Celtic midfielder Shunsuke Nakamura.
The Japanese playmaker floated in a free kick and with Australian goal keeper Mark Schwarzer being felled by Japan’s Naohiro Takahara the ball bounced untouched into the vacant net.
Egyptian referee Essam Abdullah el Fatah allowed the goal to stand, much to the dismay of the protesting Australians.
What made the decision even stranger was el Fatah’s keenness to blow the whistle at even the slightest contact before and after the pivotal moment.
The Australians fought hard to find an equaliser before the break with the two Mark’s Viduka and Bresciano looking the most likely.
The organised Japanese defence repelled each attack with assured ease.
Disappointment for Japan fans
Like each of the two previous matches which kicked off in the afternoon sun, the tempo dropped in the second half as the players felt the effects of the heat.
Looking to his bench for inspiration, Australian coach Guus Hiddink chose Cahill to replace Parma midfielder Bresciano and it proved to be an astute decision.
With the clock winding down and Australia’s World Cup campaign looking like it was over before it had begun, Cahill wrote himself into the record books.
Australia’s first ever World Cup goal came in the 84th minute as a long throw from Lucas Neill caused a goal mouth scramble and Cahill pounced.
The Evertonian had needed FIFA intervention to make his Australian debut after playing for Western Samoa at Under 20 level and all the paperwork was worth it when five minutes later he hit the winner after finding space at the top of the box sending the ball past Japanese keeper Yoshikatsu Kawaguchi.
It's on the way
Neither the Australian players nor fans could believe it as they found themselves in front with minutes to spare.
The celebrations began early when Aloisi, the man who had sent the side to the World Cup with his winning penalty against Uruguay, capitalised on the advancing Japanese attack to seal his side’s historic win.