A victory would have handed the Socceroos a spot in the world tournament for the fourth consecutive time.
Instead, the defeat has football analysts studying the permutations of what could happen ahead of next week's final round of qualifiers.
Despite the tantalising prize on offer, this match was never going to be an easy proposition for Australia.
The Socceroos were away from home, playing in front of a full stadium --- tickets were going for around $500 at one point -- and facing a Japanese team with the same prize in sight.
Along with that, Japan's coach was reportedly on the verge of being sacked.
It did not get any easier on the day of the game, when Socceroos playmaker Aaron Mooy woke up ill and could not take his place in the team.
And after a good Japanese start to the game, things got very hard, indeed, for Australia in the 41st minute, when a good Takuma Asano run beat the Socceroos' defensive line.
And the Samurai Blue sealed Australia's fate -- and their own sixth consecutive World Cup appearance -- in the 82nd minute of play.
It came after a magnificent pass and run, and Yosuke Ideguchi's finish was a goal worthy of sending a team to sport's biggest stage.
That was the game finished, but the questions remain.
Socceroos coach Ange Postecoglu told Fox Sports the blame for what happened should go on him and no-one can tell what difference having Mooy might have made.
"Who's to say? We just don't know. But the team we put out there was certainly good enough to get the job done. So, I'll take responsibility for the team selection, the way we play. Tonight's result is on me, not the players or the ones who are missing. We didn't have the night we wanted to."
Postecoglu says he hopes Mooy will be fit for Tuesday night's (sept 5) final qualifier against Thailand in Melbourne.
It could be crucial, because Postecoglu says Australia did not control enough of the game against Japan, pointing to the midfield -- Mooy's area -- in particular.
Despite the task now in front of the Socceroos, he has told Fox Sports he is optimistic about that game, although it will take more for Australia to qualify for next year's World Cup.
"Being at home will make a difference. And, yeah, we've got to win. And, unfortunately, we've got to rely on another result. But we'll do our job and see what happens. Look, at the moment, I'm just disappointed about tonight. The rest of it's secondary."
Australia plays Thailand on the final match day, while Japan, already qualified, plays at Saudi Arabia.
Australia has to better Saudi Arabia's result -- and possibly thrash Thailand in doing so -- to take second spot in the group and automatically qualify for the World Cup.
Otherwise, the Socceroos could end up in third, which would mean a two-legged playoff against the third-place team in the other Asian group.
That could be South Korea, Syria, Uzbekistan or China.
The winner of that playoff would play the fourth-place team from the North and Central American region in another two-legged playoff in November.
The winner of that playoff then qualifies for the World Cup.
In an extreme, unlikely case, the Socceroos could end up in fourth in their group if they lose to last-place Thailand and could be eliminated from World Cup consideration right then.
Socceroos midfielder Jackson Irvine has told Fox Sports the side will still be doing everything it can.
"Obviously, we're extremely disappointed. But it's not finished yet. We can still go to Melbourne (and beat Thailand). It's going to be difficult now. But as long as it's mathematically still possible, we're going to be giving it everything we've got."
