The victor of the playoff will face the fourth-placed team in CONCACAF (currently Panama) in a two-leg contest to secure a spot at next year's World Cup.
But the home team were rocked in the sixth minute of the reverse fixture when Omar Al Somah, dubbed the Syrian Zlatan Ibrahimovic, capitalised on a mistake from Mark Milligan and fired the minnows into a shock lead.
Without five first-choice players through injury or suspension, they also had to play most of extra time with 10 men after midfielder Mahmoud Al Mawas was dismissed for two yellow cards.
In a world Cup qualifier against Syria Tiny Tim scored both Socceroo goals in a 2-1 win. Eventually that goal came and it was that man again Cahill who was in the right place at the right time.
For a second we actually thought Syria could do it and watching the game play out on Twitter was almost as good as watching the game itself.
As penalties beckoned, Robbie Kruse sent over a cross from the byline and Cahill out-jumped his marker to power a header past the diving Ibrahim Alma.
And while that sounds positive, Australia still needed to step up the intensity to ensure it progresses with certainty.
Tim Cahill of Australia (left) celebrates with teammate after scoring against Syria during the match, played in Sydney. The Aussies will face the fourth-placed side in the "Hex", with USA, Panama or Honduras all potential opponents for them next month.
Manager Ange Postecoglou had been forced into a change in the 11th minute, having to bring Aaron Mooy - a shock bench starter - into the fray for the injured Brad Smith. If it does, the two games will be Postecoglou's last in charge of the national team.