Defender Ali Salmeen deflected Ajdin Hrustic's volley past Khaled Eisa with six minutes remaining at Al Rayyan's Ahmad bin Ali Stadium to keep Australia's hopes of qualifying for a fifth consecutive World Cup finals alive.
Jackson Irvine had put Graham Arnold's side in front with a close-range strike in the 53rd minute but Caio Canedo levelled four minutes later with an emphatic finish into the roof of Mathew Ryan's net.
The Australians increased the pressure throughout the second half and it eventually paid off when Hrustic volleyed towards goal following Aaron Mooy's corner and the deflection off Salmeen proved decisive.
"We showed good character, I think we dominated the majority of the game and we took the chances when they came," said Australia's Martin Boyle.
"It's only a job half done. We have to dust ourselves down, prepare and we will go again."
Harib Abdalla Suhail had carried the principal threat down the left for an Emirates side that had the better of the initial exchanges, forcing Ryan into a pair of saves at his near post in a tepid first 45 minutes.
But eight minutes into the second half the Australians struck, with Boyle turning the defence before finding Irvine, who scored with a first-time finish from inside the six-yard box.
The lead lasted four minutes as Suhail's pace proved problematic once more. The Shabab Al Ahli winger curled in a cross and Caio eventually drove his left-foot shot into the roof of the net.
Craig Goodwin and Hrustic both had efforts that flew over the target before Boyle saw the ball bounce off his shins and go wide as the Australians increased the pressure.
Eisa kept the Emirates in the game with an instinctive save from substitute Jamie Maclaren 10 minutes from time, but there was little he could do four minutes later.
Mooy's corner was headed back towards the edge of the penalty area and Hrustic made a powerful connection, with the ball taking a decisive deflection off Salmeen's hip to leave Eisa helpless.
The Socceroos will meet Peru in the same venue next Monday in the first of two intercontinental playoffs to determine the remaining spots at the finals, with New Zealand playing Costa Rica in the final eliminator 24 hours later.