Hong Myung-bo's side fell behind in the 58th minute when Czech defender Ladislav Krejci powered home a header from a set piece. But South Korea responded quickly as midfielder Hwang In-beom equalized nine minutes later before setting up substitute Oh Hyeon-gyu for the winner in the 79th minute.
The victory earned South Korea three points and left it level with co-host Mexico, which defeated South Africa 2-0 in the tournament's opening match earlier in the day.
After a cautious first half dominated by Korean possession and several half-chances for captain Son Heung-min, the match sprang to life after the break.
Czechia repeatedly threatened through its aerial strength and was rewarded when Krejci rose above the Korean defense to head home the opener.
South Korea responded through Hwang, who calmly finished after a well-worked move involving Lee Kang-in. Moments later, the Czechs thought they had regained the lead when Tomas Soucek found the net, only for the goal to be ruled out for offside.
The momentum shifted decisively in Korea's favor. Hwang burst beyond the Czech back line before delivering a low cross that Oh converted from close range to complete the turnaround.
Goalkeeper Kim Seung-gyu, criticized for failing to stop Krejci's header and nearly gifting away possession earlier in the half, redeemed himself with two crucial saves in the closing stages. The veteran goalkeeper produced a pair of full-stretch stops, including a dramatic save from Michal Sadilek in stoppage time, to preserve the lead.
Hwang was widely regarded as the player of the match after contributing both a goal and an assist.
The victory marked South Korea's fourth opening-match win in World Cup history and its first since the 2010 tournament in South Africa.
South Korea, appearing in its 12th World Cup finals, is seeking a third appearance in the knockout stage at an overseas World Cup following runs in South Africa in 2010 and Qatar in 2022.
The Koreans will next face Mexico on June 19 before concluding Group A play against South Africa on June 25.
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