A second-half goal from Brett Holman was enough to give the Socceroos three points from a scrappy performance, and take them through with 12 points from five games.
Australia were keen to reassert themselves after losing their 100 per cent record in Friday's shock 1-0 defeat by Oman, but they rarely gelled against a Thai side who put on a fighting display for their fans.
A near-capacity crowd at Supachalasai National Stadium provided buoyant support for the hosts.
And Thailand marginally shaded the first half as Australian left-back Michael Zullo endured a torrid evening against the pace and aggression of winger Suree Sukha.
Thailand wasted two good chances to score before the interval, both coming from diagonal balls behind Zullo.
At the other end, goalkeeper Sinthaweechai Hathairattanakool was equal to anything Australia's burly strikeforce could throw at him, saving well from two Josh Kennedy headers and calmly claiming a number of crosses under pressure.
But with 15 minutes to go, a cross from former Blackburn Rovers man Brett Emerton on the right found Holman unmarked six yards out, and the latter made no mistake with his header.
Australia are now assured of joining Asian champions Japan, Uzbekistan and Jordan in the final round of qualifying.