Singapore went ahead against the run of play 38 minutes into a scrappy game when Aleksandar Duric, A 39-year-old former Olympic canoeist, leapt high in the air to connect with a corner and beat the keeper from close range.
Thailand looked nothing like the side which beat Singapore 3-1 away on Saturday and paid the price for some sloppy defending and wayward finishing.
Teerasil Dangda came close to levelling the score in first-half stoppage time when he skipped round two defenders but shot just wide of the far post.
The hosts went all out for an equaliser and continued to dominate after the break, but Teerasil, Suchao Nutnum and Pipat Tongkanya each squandered perfect scoring chances before Singapore packed out their defence to keep them at bay.
The win moved Singapore into second place in Group E with six points, leaving Thailand third on five. Iran lead on seven, with the top two qualifying for the finals in Qatar 2011.
"The competition is now really open and we now have a better opportunity to qualify," Singapore coach Raddy Avramovic told reporters. "We had the discipline, we defended well and that's what's it's all about."
Robson rued his team's poor marking in his first defeat as Thailand coach but said he was confident they would still qualify.
"I'm very disappointed - it should have been 0-0," Robson said. "It was a lapse of concentration and a very costly one. It's not over yet and we still have a good chance to qualify."
