Second-half substitutes Tana Chanabut and Adisak Kraisorn finished off the Taiwanese who stunned the hosts shortly after the kick-off.
With the victory, Kiatisak Senamuang’s men consolidate their position at the top of Group F with 13 points from five matches and move closer to a berth in Asia’s last-12 team qualifying round for the 2018 World Cup.
Iraq have five points from three matches and will next play Taiwan on Tuesday (Nov 17). The Iraqis will also host Thailand on March 24.
Vietnam are third in the group with four and Taiwan fourth with no points.
The eight group winners and four best runners-up will progress to Asia’s final qualifying round for Russia 2018.
Thailand were forced to make two changes to the side that routed Vietnam 3-0 in Hanoi last month with Suttinun Phukhom taking the field to replace injured Korawit Namwiset and Sanrawat Dechmitr coming in for Chanathip Songkrasin.
More than 50,000 fans turned Rajamangala into a blue sea but they were all hushed into silence in the second minute when Taiwan went ahead.
Lin Che-Yu hit a corner and Yen Tavio broke free from his marker to squeeze a precise header past defender Tristan Do and goalkeeper Kawin Thamsatchanan.
The goal put the visitors in defensive mode and it didn’t help as well that the Thais concentrated more on moving the ball around in the midfield rather than making any meaningful inroads.
Midfielder Pokklaw A-Nan saw his long shot fly over the bar and and a few minutes later a free-kick by Theerathon Bunmathan also missed the target.
Taiwan also had an opportunity to widen the gap but Lin Chang-Lun was denied by Kawin.
Thailand should have scored when Tristan created an opening for Kroekrit Taweekarn whose shot hit the bar.
The home team’s efforts finally paid off when they equalised in the 40th minute.
Taiwan’s defenders let a cross from the left by skipper Theerathon sail unchecked to Thailand’s prolific striker Teerasil Dangda to head home comfortably.
The hosts upped the tempo of their attacks but were unable to pierce through Taiwan’s defence and the two sides went into the break tied 1-1.
Thailand played an improved game in the second half and were rewarded when Teerasil slipped a bisecting pass to Pokklaw who successfully beat an off-side trap to guide the ball into the net and put his side ahead.
Taiwan cancelled out the home team’s advantage in the 65th minute when Wu Chun-Ching set up unmarked Hung Kai-Chun, whose shot left Kawin with no chance.
Then Adisak and Tana rose to the occasion for the hosts and took charge.
Tana, a 70th-minute replacement for Kroekrit, picked up a long ball on the left and swiftly moved into the box before slipping it to Adisak, a 63rd-minute substitute, to net from close range to make it 3-2.
Two minutes later it was all over for the Taiwanese when Theerathon’s free-kick was deftly headed into the far right corner by Tana.
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