The Lions threw on top scorer Ilhan at half-time for Kweh, with Anuar moving to the right.
There was no let-up from Thailand after the break, extending their lead in the 50th minute through Seksan.
A loose pass from Tan was cut out by the Thai midfield, before Patrik Gustavsson – who had come on for Teerasak in the first half – outpaced Tan and crossed for Seksan, who finished cleanly.
Lee brought on Ryhan Stewart for Tan in the 56th minute.
Ilhan stole in behind the Thai defence in the 59th minute and nearly rounded the keeper, before he was called back for offside.
The Lions had more possession, but their final ball was lacking at most times and the Thai defence was hardly threatened.
Thailand pushed Singapore on the counter, and in the 64th minute, Izwan was called into action with a good save after a one-on-one with Picha Autra.
Ilhan was not to be denied his goal and in the 83rd minute, he curled a shot into the bottom corner of the goal from outside the box, drawing loud cheers from the crowd.
Singapore pressed for another goal. Despite the late rally, the Lions failed to test Kampol properly and the Thais ran out winners.
Thailand head coach Anthony Hudson said his players put in a solid performance.
“Proud of the guys against a very difficult opponent, but also we’re very clear that it is only half-time, and we need to go back to Bangkok and make sure we deliver an even bigger performance,” he added.
He said Singapore were a “complicated team” to play against and that the way the Lions were set up made it very difficult to build pressure against them.