There were no problems for Japan in Saitama, however, as Takuma Asano, in the first half, and a brilliant Yosuke Ideguchi strike eight minutes from time were enough to see off Australia 2-0.
The 2-0 victory means Japan now join the already qualified Brazil and Iran, along with hosts Russian Federation, at the World Cup next June.
Yuto Nagatomo set up the first goal in 41st minute, sending a cross into the box that an unmarked Asano calmly side-footed past Australia goalkeeper Mathew Ryan. But with a 2-1 loss to the United Arab Emirates, Japan and Australia entered their game this morning knowing that a win would either clinch qualification for Japan or all but clinch for Australia.
But given that the dates of the Muslim pilgrimage of Hajj meant the Saudi Arabia-UAE game was played two days earlier than the other Group B encounters, both Japan and Australia now have the advantage of knowing exactly what is on the line at Saitama Stadium.
The war-torn country's national soccer team beat Qatar 3-1 in Malaysia, moving into third place in Group A of Asian qualifying.
Australia have appeared at the last three World Cups, reaching the knockout stages in 2006 with a golden generation of players such as Mark Viduka, Harry Kewell and Tim Cahill.More news: When is Eid al-Adha 2017?
Ange Postecoglou's men must win big against Thailand in Melbourne, all the while banking on the Blue Samurai taking points off Saudi Arabia in Jeddah.
Japan nearly made the flawless start when Hiroki Sakai met Ideguchi's second-minute corner with a thumping header that just missed the target, before Takashi Inui cut inside and tried his luck in the 14th minute.
"We didn't have the night we wanted to".
As it stands Australia are level with the Saudis on 16 points but sit third on goal difference, so a heavy win against Thailand may well do it for the Socceroos.
"It's a result on me not on the players or the ones who were missing".
"I don't know how Australia are going to come at us but we are going to be more offensive and aggressive than the last away game against them", Japan defender Maya Yoshida told Kyodo.
"And, of course, once the ball hit the net for my goal, I was, frankly speaking, absolutely delighted".