Struggling early on to deal with Syria's pressing, the Socceroos wasted a golden chance to grab the opener as Jamie Maclaren headed wide in the 21st minute when he should have done better after being picked out by Rhyan Grant.
Syria would then find the back of the net on 30 minutes after a set-piece only for a foul on Mark Milligan in build-up to deny them.
Six minutes later Maclaren would twice force saves out of Syria's keeper Ibrahim Alam after he was played through on goal by Tom Rogic.
In the 42nd minute there was nothing Alam could do as Awer Mabil curled home a thumping long-range strike to hand Australia the lead.
The Socceroos advantage would last just two minutes however as Syria hit straight back through Omar Khribin, who had his initial header saved before poking home the rebound.
After the break Australia would restore their lead as a Chris Ikonomidis strike was ruled to have crossed the goal line in the 54th minute after an incisive cross from Rogic.
The green and gold were then spared what appeared to be a clear penalty for Syria in the 62 minute after the ball seemed to strike Mark Milligan's outstretched arm.
After being denied a clear spot-kick, Syria would be awarded a questionable one in the 78th minute for a foul in the box and Omar Al Somah made no mistake to pull Syria level again.
With the points set to be shared, Ikonomidis would then pick out Rogic at the top of the box in the second minute of injury-time, with the Celtic midfielder firing home to hand the Socceroos all three points.
That 3-2 win sealing second spot in Group B for Australia and sending Syria bottom to end their Asian Cup campaign.