Veteran striker Tim Cahill rued a late goal by Japan's Keisuke Honda that denied the Australians a much-needed win Tuesday in their group's final qualifying round for the 2014 World Cup.
The 1-1 result made Asian champions Japan the first team to qualify for the 2014 World Cup in Brazil, though Australia kept their hopes alive for the finals.
After Tommy Oar's somewhat lucky strike in the 82 minute, Matthew McKay handled the ball in the area to give Japan a penalty chance, which Keisuke Honda capitalised on in injury time.
"It was close to nearly a perfect performance, coming away and nicking a win and we were unlucky in the end. It was a tough game playing these guys as they are a good team," Cahill was quoted as saying by Kyodo News.
"I thought we created some good chances and still defended really well. I think when you look at it we probably would have taken a point beforehand but it's just hard to take conceding a penalty. It happens in football."
"At the end of the day you can't change it and we have to deal with it. There are always doubts, but it happens."
Australia will now play Jordan on June 11 and Iraq on June 18, both at home, hoping for an automatic qualification position of second in Asian qualifying group B.
However, Australia's task was complicated when Oman beat Iraq 1-0 to rise to second in the group.
The Socceroos have two home games left, against Jordan and Iraq, while Oman have only one to play away against Jordan on June 18.
"We have had a good point. I thought we played really well and need the same thing again," said Cahill.
Australia coach Holger Osieck said: "When Honda is on the pitch he always makes a difference. He's always a player you have to be aware of. That's a fact."