Robbie Kruse's first-half goal looked to be enough, but Syria came back to secure a draw with a late penalty in their World Cup qualifier.
Ange Postecoglou made five changes to his Australia squad to face Syria, with captain Mile Jedinak left out.
It has been a long time coming but Nikita Rukavytsya is back in Australia's squad for next month's World Cup play-off against Syria.
Bert van Marwijk secured World Cup qualification for Saudi Arabia but he has been replaced by Edgardo Bauza.
Chief executive of Football Federation Australia David Gallop believes Ange Postecoglou can still guide the Socceroos to the World Cup.
Unspecified breaches of competition rules will be investigated by the AFC following its final round of qualifying matches for Russia 2018.
Australia must settle for a play-off tie with Syria after Saudi Arabia beat Japan 1-0 to snatch a place in the World Cup group stage.
Omar Al Soma was Syria's hero as his equaliser deep into stoppage time against Iran sealed a World Cup qualification play-off place.
There were no goals, but South Korea's draw in Uzbekistan means they are heading for a ninth consecutive World Cup appearance.
Australia are close to sealing a World Cup place after a thrilling 2-1 home win over Thailand.