Australia had never secured a victory on Japanese soil, but a stroke of luck came their way when Shogo Taniguchi accidentally scored an own goal just before the hour mark. The surprising turn of events gave the visitors a shock lead in front of a sizeable crowd of nearly 60,000 spectators.
Cameron Burgess scored a Socceroos own goal at the other end eight minutes later to hand Japan an equaliser that keeps them on top of Group C on 10 points from four games.
Australia moved to five points, having taken one win and one draw in two games since new coach Tony Popovic replaced Graham Arnold in September.
“To be honest, I wanted to win at home,” Japan coach Hajime Moriyasu said.
“I wanted to deliver a victory because so many supporters came to the stadium and many supporters were cheering for us in front of the TV.
“However, the fact that we were able to fight without collapsing after conceding the first goal... I think that the fact that we were able to gain one more point without giving up, the three points is a step forward.”
Japan went into the game with a perfect record of three wins, with 14 goals scored and none conceded at this stage of qualifying. The draw ends their run of consecutive wins in World Cup qualifying in total at nine.
Australia’s preparations, meanwhile, were hampered when they arrived at Saitama Stadium later than scheduled after their team bus got stuck in traffic.
Popovic handed a first cap to 34-year-old Luke Brattan, who started alongside captain Jackson Irvine in midfield.
Brattan was one of six changes to the line-up that beat China 3-1 at home last week in Popovic’s first game in charge.
Liverpool’s Wataru Endo was missing from Japan’s squad and was replaced as captain by fellow midfielder Hidemasa Morita.
Takefusa Kubo gave Australia problems down the right wing and he hit the side-netting after a dangerous move in the sixth minute.
Japan dominated possession but struggled to create clear-cut chances for the rest of the first half, with a deflected Kaoru Mitoma shot their best effort.
Takumi Minamino headed wide at the back post as Japan started the second half with the same attacking intent.
But Australia took a shock lead just a minute later when Sint-Truiden defender Taniguchi turned Lewis Miller’s cross into his own net on 58 minutes.