It was the third straight loss for Thailand in the eight-team, round-robin qualifying tournament.
In other Group A matches Thursday night, South Korea defeated Qatar 3-2, Syria dropped China 1-0 and Iran defeated Uzbekistan 1-0.
Thana Chanabutr scored Thailand's only goal in the 65th minute of the match.
By then, the UAE had built up a solid lead with goals by Ali Ahmed Mabkhout in the 14th and 47th minute. Ahmed Khalil added the insurance goal three minutes into stoppage time.
Thailand play at Iraq next week.