The result was a disappointment for a favoured Korean side playing its first match since the sacking of coach Jurgen Klinsmann. Belated revelations of a physical bust-up between two of their stars, Lee Kang-in and captain Son Heung-min, have further sapped morale, reports the Bangkok Post.
With under-23 coach Hwang Sun-hong taking charge following the dismissal of Klinsmann, the hosts took the lead three minutes before half-time at Seoul World Cup Stadium.
Tottenham Hotspur attacker Son was the man on the spot, turning in from close range to put the hosts on the way to a third qualifying win from as many matches.
But the capacity crowd was stunned into silence on 61 minutes when Suphanat Mueanta stayed onside to rifle a shot past exposed goalkeeper Jo Hyeon-woo to give the War Elephants the equaliser.
South Korea had several chances to score the winner, but they failed to take them against an increasingly overworked Thailand defence.
South Korea, ranked 22nd in the world, remain atop Group C in the Asian Football Confederation (AFC) qualification with seven points, while 101st ranked Thailand remain in second place with four points.
There are nine groups of four in the current second qualifying round. The two best teams from each group will advance to the third round.
The two sides will meet again on Tuesday at Rajamangala National Stadium in Bangkok.
The other game in Group C yesterday saw China and Singapore share a 2-2 draw.