The Socceroos looked destined to take a 1-0 win away from Saitama, before a handball by Matt McKay handed Keisuke Honda a spot kick he duly converted
Tommy Oar's fortunate goal - his first at international level - in the 82nd minute appeared set to give the Socceroos a stunning three points in the World Cup qualifier, 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, who have qualified for Brazil 2014 as a result, while Australia are well-placed to follow them out of Group B ahead of home games against Jordan and Iraq.
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, but goalkeeper Mark Schwarzer appeared to have the effort covered.
The Socceroos were then 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 Tim Cahill.
Australia were 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, who dictated the tempo and were able to keep possession for longer periods in the middle part of the half.
And the chances followed, with Kruse denied by a stunning Eiji Kawashima save in the 34th minute when put through by Holman, before Cahill fired the rebound over the bar.
Japan controlled possession after the interval, with Honda and Kagawa again looking 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, before Honda watched two free-kicks from similar spots just outside the area fly over the bar and straight at the Fulham shot-stopper.
Japan dominated the half but Australia created a glorious chance with a quarter of an hour left to play. 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 to set up a grandstand finish.
Tommy Oar continued to run at defenders and his cross-cum-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, and Honda fired the penalty straight down the middle to secure his side's place in Brazil next summer.