After a lacklustre first half in which both teams were jeered as they left the field, the Czech Republic took the lead in the 59th minute on Thursday night (Friday AEST) via a header from captain Ladislav Krejci after a long throw-in into the penalty area.
South Korea equalised in the 67th minute when Hwang scored after faking a shot with a nifty move to clear two Czech players.
Hwang then made the cross from the right flank for Oh Hyeon-gyu's decisive strike in the 80th minute in a match played in front of hundreds of empty seats at Guadalajara Stadium.
Led by star forward Son Heung-min, South Korea controlled possession and outshot the Czechs, who were making their first World Cup appearance since 2006.
The Koreans, ranked 25th by FIFA, had most of the significant scoring chances against the 38th-ranked Czechs but failed to capitalise early.
Son was looking to become South Korea's top goal-scorer at the World Cup and the Asian player with the most goals in the tournament.
The 33-year-old former Tottenham star, who now plays for Los Angeles FC in Major League Soccer, entered Thursday's match having scored three goals over three previous World Cups.
Appearing in his fourth World Cup, Son had a couple of good opportunities to add to his tally but missed wide in the first half and had a close-range shot saved in the second.
The Czech Republic thought they had retaken the lead with another set piece in the 77th minute, but Tomas Soucek was ruled offside on his header.
Czech Republic coach Miroslav Koubek said "probably the better team won", but added his side could have had a better outcome if not for "some mistakes".
"We played very well, it could have been a draw and we could have won as well," Koubek said.
The announced attendance was 44,985 at the 45,664-capacity Guadalajara Stadium, a crowd that included FIFA president Gianni Infantino. Sections in the middle of the stands had many unoccupied seats, and there were other empty spots scattered across the stadium.
South Korea are making their 11th straight World Cup appearance and 12th overall, the most of any Asian country. Their best result was a fourth-placed finish at the tournament they co-hosted with Japan in 2002. Since then, the South Koreans have never gone beyond the round of 16.
In the other Group A match on Thursday, co-hosts Mexico defeated South Africa 2-0 in the tournament opener in Mexico City.
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