Playmaker Chanathip Songkrasin gave the War Elephants a 1-0 lead after seven minutes but Brendan Gan equalised 26 minutes into the match. Mahamadou Sumareh sealed the victory for the host seven minutes into the second half.
Thailand have never beaten Malaysia at the 87,000-seat stadium in four meetings with two losses and two draws.
The defeat dropped Thailand to second in Group G of Asia's second qualifying round for the 2022 World Cup after Vietnam edged the United Arab Emirates 1-0 in Hanoi to lead the standings.
Thailand began their campaign with a lacklustre home draw against Vietnam but bounced back with wins over Indonesia in Jakarta and the UAE at Thammasat Stadium in Rangsit. They will play an away game in Vietnam on Tuesday (Nov 19).
The eight group winners and four best runners-up advance to the continent’s 12-team final qualifying stage for the 2022 finals.
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