The province’s Thien Truong Stadium, with a seat capacity of 20,000, was nearly full.
Patrik Gustavsson gave Thailand the lead at the 33rd minute. However, Thai youngster Jonathan Khemdee was sent off for a challenge on a Malaysian player before half-time.
Danial Asri equalised for Malaysia in the 61st minute.
The match looked set to finish in a draw, until an own goal by Thai defender Anusak Jaiphet in the injury time settled the 2-1 win for Malaysia.
Laos drew 2-2 with Singapore in another match of Group B.
