Saudi substitute Fahad Al Muwallad scored a spectacular winner for Bert van Marwijk's side, who qualified for the first time since 2006 with victory over a Japan team that had already reached the finals.
The result pushed Australia into third in Group B and a place in the playoffs, where they will meet Syria, who drew 2-2 with Iran to finish third in Group A.
South Korea's Lee Keun-ho, Son Heung-min and Lee Dong-gook all hit the woodwork but it mattered little as they earned a point that sealed second place in Group A of Asia's qualifying competition behind the already-qualified Iran.
Syria took third spot in the group when Omar Al Soma's late goal earned Ayman Hakeem's side a dramatic draw with Iran that pushed Uzbekistan out of the playoff positions.
Syria took the lead in Tehran and became the first team to score against Iran in 13 qualification matches when Tamer Haj Mohamed netted from close range after Al Soma's free kick had been fumbled by Iranian goalkeeper Alireza Beiranvand.
A double from Sardar Azmoun looked to have given Iran all three points until Al Soma - playing only his second match for Syria since his return from a self-imposed exile - slid the ball through Beiranvand's legs to level deep into stoppage time.
The draw meant Syria finished level on 13 points with Uzbekistan but took third place on goal difference.
LARGE MARGIN
Australia had gone into their meeting with Thailand knowing they needed to win by a large margin to put pressure on Saudi Arabia, who were hosting Japan in Jeddah several hours later.
Ange Postecoglou's team were made to work hard for the three points against a Thai side that packed the defence.
Tomi Juric gave the Socceroos the lead after 69 minutes only for Pokklaw Anan to pull Thailand level against the run of play.
Mathew Leckie restored Australia's lead but, with only a one-goal advantage secured, the atmosphere at AAMI Stadium fizzled out at the end.
Postecoglou's side later paid a heavy price for their inability to convert numerous chances as the Saudis squeezed past Japan.
After a tense first half, livewire substitute Al Muwallad changed the complexion of the game in Saudi Arabia's favour and it came as little surprise that it was the Al Ittihad winger who broke the deadlock in the 63rd minute with a fearsome shot.
The win moved Saudi Arabia into second place in the group after Japan secured top spot last week with victory over Australia.
The United Arab Emirates saw their slim hopes evaporate with a 1-0 loss to Iraq thanks to Aymen Hussein's goal while China's chances of appearing at the World Cup went the same way despite a 2-1 win over Qatar.
Marcello Lippi's team came back from going a goal behind to Akram Afif to claim all three points, but it was not enough for the Chinese to haul themselves into the playoff places.
Xiao Zhi and Wu Lei scored for Lippi's team, who have won three of their last five games but fell a point short of maintaining their World Cup dream.
(Reporting by Michael Church, Editing by Toby Davis)
