The point took Australia into second place in Asian zone Group B qualifying on goal difference going into its final two qualifiers against Jordan and Iraq later this month as it gets set to punch its ticket to Brazil.
The outcome suited Japan, which qualified for the World Cup as a result. Whizkid Oar pounced in the 81st minute, his looping cross from the left evading the flapping fingers of keeper Eiji Kawashimi as it dipped into the net. But joy turned to despair on the stroke of full time when Matt McKay was penalised for handball and Keisuke Honda buried the spot kick.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Australia played with patience and poise, mixing long balls in the direction of lone striker Tim Cahill, with playing out from the back.
Holgar Osieck's men were also biting in the tackle, restricting the space available for the Blue Samuari's purists to operate in as a yellow brick wall guarded the away goal.
The Socceroos also rode their luck in front of a 60,000 crowd baying for the home side to break the deadlock.
Osieck made five changes from the team that drew 2-2 with Oman in March with captain Lucas Neill and Sasa Ognenovski returning in defence, Mark Milligan and Mark Bresciano drafted into the centre of midfield and Tommy Oar unleashed for this first start in a World Cup qualifier on the left flank.
As expected, skipper Lucas Neill - suspended against Oman, and Sasa Ognenovski - dropped for that match - were reunited at the back as Osieck opted for experience.
J-League based striker Josh Kennedy - chasing his first Socceroos start in 17 months after batttling back from injury - had to be content with a place on the bench, while Mile Jedinak, Alex Brosque and Michael Zullo missed out through inury.
That left Cahill - Australia's master of international rescue - to lead the line with Brett Holman tucking in behind, and Kruse on the right and Oar on the left, providing the width.
Going into the game needing just a point to become the first team to clinch its ticket to Brazil, Japan coach Alberto Zaccheroni unleashed a full strength line up boasting all the big guns - Yuto Nagatomo, Yasuhito Endo, Keisuke Honda and fellow midfield magician Shinji Kagawa.
And Endo had the chance to cause an alarm in the sixth minute, but his 25 metre free-kick drifted just wide after Ognenovski had been penalised for a foul on Shinji Okazaki.
Then in the 12th minute defender Maya Yashida wasted a free header from a Honda corner, much to Australia's relief. Midfielder Endo then fired just over from the edge of the area before a neat build-up involving Kruse and Cahill saw Holman steer his shot wide at the other end when well placed.
Goalkeeper Mark Schwarzer rescued Australia in the 18th minute when a clever passing move orchestrated by Honda opened up the Socceroos up and it took a one-handed stop from the veteran No.1 to repel Kagawa.
Growing in stature as the game progressed, Australia might have broken the stalemate in the 34th minute when a raking through ball from Brett Homlan was latched on to by Kruse who was denied by onrushing goalkeeper Eiji Kawashimi.
Japan threatened again early in the second half, Kagawa crossing deftly for Honda to prod just wide in the 54th minute. Two minutes later Kagawa cut inside Luke Wilkshire and clipped a shot which grazed the post with Schwarzer beaten.
Osieck made his first change in the 72nd minute, with Holman giving way to Dario Vidosic.
Cahill was denied by a superb block from Yoshida after a Kruse cut the ball back invitingly in the 75th minute in a rare burst forward by the visitor.
It took another great stop with Schwarzer to defy wideman Yuto Nagatomo 12 minutes from time. And then came Oar's moment before Honda replied.
Socceroos XI: Mark Schwarzer, Luke Wilkshire, Lucas Neill, Sasa Ognenovski, Matt McKay; Robbie Kruse, Mark Milligan, Mark, Bresciano, Tommy Oar, Brett Holman (Dario Vidosic 72'), Tim Cahill.
Japan XI: Elji Kawashima; Yuto Nagatomo, Maya Yoshida, Yasuyuki Konno, Atsuto Uchida (Mike Havenaar 86'); Yasuhito Endo, Makoto Hasebe; Shinji Kagawa, Keisuke Honda, Shiji Okazaki (Hiroshi Kiyotake 88'); Ryoichi Maeda (Yuzo Kurihara 80').
