South Korea joined them and Japan in qualifying for the finals after sneaking through on goal difference and Uzbekistan and Jordan retained hope of making it five Asian sides in Brazil after taking the third spots in the groups to set up a play-off.
The teams will meet over two legs in September with the winners taking on the fifth-placed side in South America in a similar play-off in November for a place at the finals.
That route was something most Australian fans were facing as their match against Iraq remained goalless with only seven minutes remaining and leading goal threat Tim Cahill having been substituted.
His replacement, though, turned out to be the saviour as Josh Kennedy, representing his country for the first time in over a year, was left free to head home a cross from the right and hand the Footballoos the win that secured a third consecutive finals appearance.
"At times you reach a phase in a game where you have to make things happen and it was about the time," Australia coach Holger Osieck told reporters after booking second place behind Japan in Group B.
That time never came for South Korea but a ninth appearance will as they slipped through on goal difference despite a 1-0 home loss to Iran in Group A.
The build-up to the match had seen Korea coach Choi Kang-hee going on the offensive, stating his side would beat Iran after he claimed to have been "badly treated" in the reverse fixture in Tehran last year.
The Koreans only needed a draw to ensure another appearance at the finals but they pushed and pressed for the win with their abundance of attacking talent, only to come unstuck against an assured Iranian backline.
Choi had said he would step down once qualification was assured and the coach was in no doubt his reign had been poor after a number of disgruntled voices in the Ulsan crowd watched one of Asia's most talented sides stutter over the line.
"I would like to express gratitude to the players who had hard times due to a bad coach," Choi said in a televised interview.
Choi had said that Uzbekistan were going to join them in qualifying but it was Iran who topped Group A, leaving Carlos Queiroz to enjoy the last laugh after the "bad manners" row.
"We were technically superior and decisive in the face of crisis," Queiroz said after the backs-to-the-wall victory.
The Uzbeks knew they had to record a four-goal win at home to Qatar and hope Iran drew with Korea to have any hope of sealing an automatic qualifying berth and a first finals appearance.
The home side dominated from start to finish against their already-eliminated opponents but found Qatar's debutant goalkeeper Ahmed Abonora in good form.
Eventually, though, the pressure told and five goals came in the final 30 minutes but Korea edged second place behind Iran courtesy of having a better goal difference by two.
"Life goes on and we will give our best to qualify for Brazil," Uzbek coach Mirjalol Kasimov said.
While they will start as favourites against Jordan they will not fancy the first leg trip to the King Abdullah Stadium where Jordan followed up home wins over Asian heavyweights Japan and Australia by beating Oman to pinch a play-off berth.
Ahmad Ibrahim stooped low to score a second-half header, maintaining Jordan's unbeaten home run and denying Oman a place in the play-off.
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