Australia needed a big favour from Japan - either a win or a draw in Jeddah on Wednesday morning (AEST) - to bail them out of trouble after Tuesday night's hollow 2-1 victory over Thailand.
But substitute Fahad Al-Muwallad's 63rd-minute goal capped off a frustrating night for Ange Postecoglou's men, who will have to do it the hard way to ensure a place at Russia 2018.
Australia now faces two difficult home-and-away ties - the first against war-ravaged Syria in October - to book a spot at a fourth straight World Cup.
The winner of that play-off will go on to battle North and Central America's fourth-placed qualifier in November for a spot at the global showpiece.
Despite an incredible 45 shots on goal, the Socceroos couldn't find the margin against Thailand at AAMI Park that would have seen them overtake the Saudis on goal difference - meaning a win by any score for the home side would have done the job.
They took a while to find their groove but an inspired change at the break from coach Bert van Marwijk changed the game.
Al-Muwallad was brought on up front for Mohammad Al-Sahlawi and forced a terrific save from Eiji Kawashima shortly after his introduction, then blasted home a shot from close range just past the hour mark .
It relieved palpable pressure among the 60,000 screaming fans at the King Abdullah Sports City who were hoping to see their side qualify for their first World Cup since 2006.
Japan, who qualified with last week's 2-0 win over Australia, had nothing left to play for but often looked the better side and had two certain goals cleared off the line before Al-Muwallad's opener.
But they could not produce an equaliser, consigning the Socceroos to a third-placed finish in Group B and piling even more pressure on Postecoglou's shoulders.