The Barcelona forward curled his shot past Korean goalie Jung Sung-Ryong just before half-time, with Chelsea's Oscar getting the visitors' second shortly after the break.
Neymar, 21, had been in doubt for the game after a heavy fall in training, and he was targed with some tough challenges and constant attention in front of a near-capacity crowd.
But the young idol had the last laugh at Seoul World Cup Stadium when he thumped his strike over the wall and to the right of Jung, who got a hand to the ball but could not keep it out.
The Brazilian threw up his hands in exasperation and had a few testy moments with other players, even getting into a shoving match near the teams' benches late in the first half.
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After a tepid start to the game, Neymar had taken the ball in midfield and danced through defenders before threading a pass to Oscar, whose shot travelled over the bar.
But after being brought down for the umpteenth time, Neymar took matters into his own hands as he opened the scoring with his free kick.
South Korea brought on Son Heung-Min in the 65th minute, hoping the Bayer Leverkusen winger could add some spark to the lethargic attack.
And the home side were more lively in the last half-hour, with Lee Chung-Yong heading a corner wide in the 68th minute.
It was as close as South Korea came to score in the match, as the five-time World Cup champions outclassed the hosts.