Cahill's heroics helped Ange Postecoglou's side, who were held to a 1-1 draw in the first leg, secure a 3-2 aggregate victory to end their opponents' remarkable qualifying run.
Omar Al Somah opened Syria's account after six minutes on a slippery ANZ Stadium pitch, before Cahill came to the rescue with his 49th and 50th international goals - a first-half equaliser and decisive 109th-minute header.
The result sends the Socceroos men to a final intercontinental play-off next month against the fourth-placed CONCACAF finisher, likely Panama or Honduras.
Twenty qualifying matches over 28 months of gruelling travel to far-flung parts of Asia all came down to this breathless, slightly skittish affair that had the 42,136 crowd in raptures at times and stunned silence at others.
The odds were stacked against Syria, who made do with a heavily depleted squad at a venue historically favouring their better-resourced Australian hosts.
Disaster struck anyway not six minutes in when Mark Milligan turned over possession and, after a swift counter-attack, Al Somah popped the ball over Mat Ryan's head with ease.
The away goal advantage was gone in an instant and Australia's woes soon compounded when Brad Smith went down with an apparent hip injury.
Suddenly Aaron Mooy was warming up and on the pitch, his hugely controversially omission lasting a mere 10 minutes.
The equaliser, though, came from the veteran famous for making magic when the chips are down.
Cahill was already planning his run into the box when Tom Rogic unleashed Mat Leckie, who placed a perfect arcing cross on a platter for the 37-year-old to head home with trademark gusto for goal number 49.
Australia's attack was fluid, Aaron Mooy the fulcrum and Rogic the centrepiece, the Celtic star running through red-shirted defenders and sending one particularly venomous shot whistling just shy of the right-hand upright.
Leckie, restored to right wing-back, followed a cute backheel with a pirouette and then stung the palms of Syria goalkeeper Ibrahim Alma.
The Socceroos pushed higher after the break, shutting down opposing forays with increasing regularity but enduring nervy moments as their visitors repeatedly won the second ball.
The introduction of Syrian hero Firas Al Khatib injected drive and composure into his country's disjointed attack.
In response, Australia pounded their penalty area and Rogic came agonisingly close to netting the winner twice in quick succession.
His frustration descended into a collective scrap as both sides searched for the deciding regulation-time goal that would not come, substitute Nikita Rukavytsya fluffing his lines and Al Khatib thwarted by the slippery surface.
Extra-time had barely begun when Mahmoud Al Mawas was shown his second yellow card and given his marching orders for a stamp on Robbie Kruse.
A man down and with penalties looming, Syria upped the time-wasting antics as Australia rallied, Rukavytsya very nearly put a volley in at Alma's near post.
Then, in the 109th minute, Mooy slipped Kruse the ball and he whipped in a cross for Cahill to bury his half-century.
A free-kick by Al Somah hit the post at the death as the Socceroos survived.
