Australia's 2-1 win puts them through from the Asian play-off 3-2 on aggregate and they will next face a team from the North and Central America region, yet to be decided, over two legs in November for a place at Russian Federation 2018.
An early through ball that completely tore apart Australia's defensive line and landed at the feet of Syrian striker Omar Al Somah resulted in a goal flying past goalkeeper Mat Ryan and the Socceroos were behind 1-0.
The war-torn country, managed by Ayman Hakeem, continue their unlikely march towards a maiden World Cup finals appearance with a 1-1 draw in the first leg meaning the tie is in the balance.
Tim Cahill scored twice as Australia came from behind to edge past Syria in World Cup qualifying. Eventually that goal came and it was that man again Cahill who was in the right place at the right time.
Robbie Kruse was put through into the area, and with his back to Cahill, twisted around to cross for the 38-year-old to head home in signature fashion for a remarkable half-century of goals in Australian colours.
"We studied the Socceroos very well and I think if we had stayed at 11 players and hadn't had that red card and hit the (post) at the end (it would have been different)".
Inside the ground, a group in the Australian section of the ground unfurled a smuggled banner with the words "Free Syria", a revolutionary slogan, which was confiscated by stewards.More news: Iceland become smallest nation to qualify for 2018 World Cup
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Australia midfielder Mark Milligan described the beleaguered national side as "outstanding", saying "they fought with everything" on the night.
When all team cohesion seems lost - as it did against Syria - individual displays like Cahill's are about all they have.
"I'm proud of everything we have done together and how we can help kids watching to follow their dreams".
The move was a huge gamble given the Huddersfield Town man was the standout in last week's opening-leg 1-1 draw.
Initially, it looked bleak for Ange Postecoglou's side.
The United States, Panama and Honduras, the three nations who could provide the opposition in the intercontinental playoff, play their final qualifiers later on Tuesday.
The Syrian team has been on a remarkable run despite being forced to play all its games in other countries.