Kuwait raced to a 3-0 lead with Theerathon Bunmathan's own goal after 24 minutes and strikes from Hussain Fadhel (60) and Hamad Aman (67).
Chanathip Songkrasin scored a consolation for the home side in the 77th minute.
In the other Group B game in Teheran, Iran hammered Lebanon 5-0.
The top two teams of each of the five qualifying groups, plus the only best third-placed side among all groups, advance to the 2015 finals in Australia.
"Kuwait played very well," said Thailand coach Winfried Schaefer.
"They were very strong physically. They also played aggressively, even after they got five yellow cards.
"We did not play well. The turning point was the second goal as our players looked down and out after conceding the goal."
Thailand were the better side in the opening minutes with striker Teerasil Dangda, who returned recently from a training spell with Spanish club Atletico Madrid, had a couple of scoring chances.
But once the visitors, who finished third in the recent Gulf Cup, found their rhythm, they proved too strong for the kingdom.
Kuwait went ahead after 24 minutes when Bader Al Mutwa went clear and beat Thailand goalkeeper Kawin Thammasatchanan. Defender Theerathon tried to clear the ball from the line only to send it into his own net.
Thailand then piled the pressure on Kuwait and their appeals for a penalty after Teerasil looked to have been tripped in the area was turned down by Japanese referee Ryuji Sato in the 32nd minute.
Thailand again started strongly in the second half and it was almost one-way traffic in the first 15 minutes.
But after the Thais squandered several chances, their poor defence was punished by Kuwait defender Fadhel who headed the ball home from a free-kick on the hour mark.
Seven minutes later, Aman effectively finished off Thailand.
Substitute Chanathip cut the deficit to 3-1 after 77 minutes with a deflected long-range shot.
Thailand threw everything at Kuwait in the final minutes but failed to score while Kuwait also had their chances with one attempt hitting the bar.
Kuwait coach Goran Tufegdzic said: "I am pleased with our performance. Our long ball worked well."
Thailand will next play Lebanon in Beirut while Iran travel to Kuwait on March 22.
Group B: Iran 5 (Reza Ghoochannejhad 25, 62, Javad Nekounam 45+3-pen, 61-pen, 80) Lebanon 0; Thailand 1 (Chanathip Songkrasin 77) Kuwait 3 (Theerathon Bunmathan 24 OG, Hussain Fadhel 60, Hamad Aman 67)
Group E: Uzbekistan 0 Hong Kong 0; Vietnam 1 (Huynh Quoc Anh 60) UAE 2 (Ahmed Khalil 8-pen, Habib Fardan 67)