The Thais lost the Group G encounter 3-1 at Zabeel Stadium in Dubai.
The UAE went into the lead through strikes by Caio Canedo Correa in the 14th minute and Fabio Virginio de Lima in the 34th.
Thailand’s Suphanat Mueanta scored in the 54th minute, but UAE got another from Mohamed Juma Eid in the 94th to put themselves in second position on the table.
The Thais had to settle for a 2-2 draw with Indonesia in their opener last week, a match from which they had expected full points.
After Monday’s game, Thailand have nine points and are third in Group G.
Vietnam crushed Indonesia 4-0 on Monday, scoring all goals in the second half, to entrench themselves at the top of the table with 14 points, followed by the UAE with 12 points. Both Vietnam and the UAE have played a game less than Thailand.
Thailand will next face Malaysia on June 15 at 11.45pm (Thailand time). Both teams have nine points, but Malaysia have played a game less.