The Socceroos looked destined to take a 1-0 win in Saitama, before a late handball by Matt McKay handed Keisuke Honda a penalty he converted to clinch a World Cup berth.
Japan joins Brazil as the only teams officially in the 2014 FIFA World Cup final field, after a stoppage-time penalty from Keisuke Honda denied Australia victory as the teams played out an enthralling 1-1 qualifying draw in Saitama on Tuesday.
Tommy Oar's fortunate goal - his first at international level - in the 82nd minute appeared to give the Socceroos a stunning three points, but Honda struck from the penalty spot in the first minute of additional time after Matt McKay handled his cross in the area.
It was a deserved point for Japan, which clinched the top spot in Group B, while Australia is still well-placed in the group ahead of home games against Jordan and Iraq to wrap up the round.
Honda started for the hosts despite being under an injury cloud, but it was one of his midfield partners who had the first sight on goal in the sixth minute. Veteran Yasuhito Endo curled a 30-yard free-kick just wide, even though Australia and Fulham goalkeeper Mark Schwarzer appeared to have the effort covered.
The Socceroos were fortunate to escape unpunished twice in a matter of minutes.
Maya Yoshida missed a glorious chance as he failed to get enough on a free header from a Honda corner, before Endo blazed over from range on 16 minutes.
The chances continued to come, and Australia's first opportunity fell to Brett Holman, who hit an effort wide after being set up by New York Red Bulls Designated Player Tim Cahill.
Australia was living dangerously and had Schwarzer to thank for being on level terms after 19 minutes. Brilliant interplay just outside the area led to a chance for Shinji Kagawa, but the Manchester United attacker scuffed his shot, and Schwarzer produced a superb one-handed save.
Surviving that led to a more composed Australia outfit, which dictated the tempo and was able to keep possession for longer periods in the middle part of the half.
And the chances followed, with Robbie Kruse denied by a stunning Eiji Kawashima save in the 34th minute.
Holman fed a wonderfully weighted through ball to Kruse, whose effort was saved by Kawashima in a one-on-one, and Cahill put the rebound well over.
Japan controlled possession in the early stages of the second half, with Honda and Kagawa continuing to look dangerous. Kagawa was unlucky not to break the deadlock just before the hour-mark when his chip from the side of the area clipped the crossbar with Schwarzer beaten.
Honda had two free kicks from similar spots just outside the area, but one went over and the other straight at Schwarzer.
Even though Japan dominated the half, Australia created a glorious chance with a quarter of an hour to play.
Mark Bresciano released Luke Wilkshire down the right and his cross found Cahill, whose shot was blocked by Yoshida.
Schwarzer denied Yuto Nagatomo before the Socceroos scored against the run of play on 82 minutes.
Oar continued to run at defenders and his cross-shot floated in at the back post as Kawashima flapped at the effort. That looked to be enough before McKay moved his body towards a Honda cross, which hit the left back's arm.
Honda's penalty was powerfully struck down the middle, seeing the teams secure a point each and Japan secure a plan ticket to Brazil next summer. The Samurai Blue will also head to Brazil in the coming week to participate in the FIFA Confederations Cup. Japan is in a stacked Group A, along with host Brazil, Mexico and Italy.