The 3-2 aggregate victory sends the Socceroos into an intercontinental playoff in November against the fourth-placed team in North and Central America and Caribbean (CONCACAF) qualifying with a World Cup spot on the line.
Cahill scored Australia's opener with a trademark header in the 13th minute but it was not until 96 minutes later that he kept alive his country's hopes of a fourth successive appearance at the World Cup finals with his 50th international goal.
"I knew I was going to score, I didn't touch the ball much but in the end I delivered," said Cahill, who has played at the last three World Cups.
"That's what I've done my whole life and I'll continue to do it."
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.
Syria, who had to play all their "home" qualifiers in Malaysia because of the security situation in their war-torn nation, fought until the very end of the match but ultimately came up short in their bid for a maiden World Cup spot.
The visitors, without five first-choice players through injury or suspension, had made the perfect start in the sixth minute to cancel out Australia's away goal advantage from the 1-1 first leg draw.
Tamer Haj Mohamad dispossessed Mark Milligan in midfield and he fed Omar Al Somah, who outpaced the Australian defence and planted the ball high in the net with his left foot.
DROPPED MIDFIELDER
Australia lost Brad Smith to injury, bringing dropped midfielder Aaron Mooy on to the pitch, but the Asian champions were back on terms in 13th minute.
Mathew Leckie broke down the right and delivered a pinpoint cross that Cahill was never going to pass up, the 37-year-old forward heading the ball home in his 103rd international.
Australia dominated the remainder of the first half, with Syrian skipper Zaher Medani blocking a Cahill shot after one flowing move and goalkeeper Ibrahim Alma force to save James Troisi and Leckie efforts.
Alma again had to be at his best to stop a fierce Rogic strike from the edge of the box after 70 minutes and the Celtic midfielder curled a shot just wide of the far post from the ensuing corner.
Rogic had another chance to clinch the winner in the 89th minute but his shot was deflected past the post and the Australians were unable to make the breathrough in normal time.
Syrian midfielder Mahmoud Al Mawas was sent off for a second yellow card four minutes into the first period of extra time and from then on it appeared only a matter of time before the Australians would break down the already weary visitors.
Robbie Kruse finally carved out the decisive chance in the 109th minute when his perfectly weighted cross to the far post found Cahill, who headed it into the top left-hand corner to the delight of the majority of the 42,136 crowd.
Al Somah had one final chance to secure passage for Syria on the away goals rule as time ran out but his brilliantly struck free kick hit the post and bounced away.
(Editing by Ed Osmond)
