It was also the first game since revelations about a bust-up between skipper Son and Paris Saint-Germain’s Lee Kang-in at the Asian Cup, where South Korea lost 2-0 to Jordan in the last four.
Son was left with a dislocated finger in the fracas at their team hotel in Qatar on the eve of the semi-final.
Lee started on the bench on Thursday but came on soon after Thailand grabbed a shock equaliser in Seoul, with Suphanat Mueanta firing in from close range just after the hour.
Despite the stalemate, South Korea are still on course to reach the next stage of qualifying for 2026 and sit top of their group with seven points from three matches.
With under-23 coach Hwang Sun-hong taking temporary charge following the dismissal as coach of the German Klinsmann, the hosts took the lead three minutes before half-time.
Spurs attacker Son inevitably scored it, turning in from close range to put South Korea on the way to a third qualifying win from as many games.
A capacity crowd at the 66,000-seater Seoul World Cup Stadium was stunned into silence on 61 minutes when Suphanat was on hand and onside to rifle past exposed goalkeeper Jo Hyeon-woo.
South Korea had several chances to score the winner, but they failed to take them against an increasingly overworked Thailand defence.
The two sides meet again on Tuesday in Bangkok.
