The atmosphere at the King Abdullah Stadium in Amman was electric after outsiders Jordan, thrashed 6-0 by Japan in June, claimed an unlikely win thanks to second-half goals by Hassan Abdel-Fattah Mahmoud and Amer Deeb.
Australia pulled a goal back through substitute Archie Thompson late on but poor finishing and frantic defending allowed Jordan to claim the memorable win.
Jordan are now in second place on four points in Group B and in one of the pool's two qualifying berths for a place at the finals in Brazil in 2014.
Japan survived early pressure from Zico's Iraq to beat them 1-0 at home on Tuesday, taking a significant step towards qualifying for the 2014 football World Cup in Brazil.
Ryoichi Maeda steered in a point-blank header in the 25th minute for the Asian champions, who lost playmaker Shinji Kagawa to a back strain an hour before kick-off.
Iraq, shock Asian Cup winners in 2007 and now under the stewardship of former Japan coach Zico, could have scored twice before Maeda struck, both times having close-range efforts blocked.
A diving header from Keisuke Honda was brilliantly tipped against the post by goalkeeper Noor Sabri in the second half.
Japan now lead World Cup qualifying Group B by eight points from Iraq, Australia and Oman, at least until Jordan host the Socceroos later on Tuesday.
Alberto Zaccheroni's side have 10 points from four matches in the final round of Asian qualifying.