After poor results saw the Samurai Blue drop to third in the continental rankings, the reigning Asian champions were grouped with the Socceroos in the final round of qualifying
The Socceroos will look to avenge their defeat at the hands of the Samurai Blue in the 2011 Asian Cup final, when they lost 1-0 in extra time on Tadanari Lee's volley strike.
Because of Japan's scheduled appearance in the 2013 Confederations Cup, Alberto Zaccheroni's side were placed in Group B's fifth slot after Iran was drawn for Group A's second slot.
Australia's position was decided only at the very end of the draw as they joined Oman Iraq, and Jordan in Group B. South Korea was selected in Group A alongside Iran, Uzbekistan, Qatar and Lebanon.
"I think [Japan] still have the same quality players as before," Australia coach Holger Osieck told Fox Sports Australia after the draw.
"It's going to be a tough one, but I'm really looking forward to it, because Japan are definitely a better-quality opponent than some of the Middle Eastern countries."
The Samurai Blue will see another familiar face when they square off against Iraq and former Japan manager Zico on September 11.
The final round of qualifying begins on June 3, 2012 and will run until June 18 of next year. The top two teams in each group will advance to the 2014 World Cup finals, while the third-place teams will go head to head in the fifth round and the winner will proceed to face a representative from Conmebol in the play-off for the chance to go to Brazil.
AFC 2014 World Cup Qualifying - Fourth Round
Group A: South Korea, Iran, Uzbekistan, Qatar, Lebanon
Group B: Australia, Iraq, Jordan, Oman, Japan