A 31st minute penalty by forward Abas Atwi proved the difference as the 146th FIFA-ranked side produced a resolute defensive display to hold off their more illustrious opponents.
Fans ran on to the pitch at the Camille Chamoun Sports City Stadium at the sound of the final whistle with some Lebanese players in tears after recording their first win over the former Asian champions.
The two sides are locked on 10 points from five matches in Group B of the third round of Asian World Cup qualifiers with Kuwait third on eight after they came from behind to beat United Arab Emirates 2-1 on Tuesday.
The top two sides in the group will reach the 10-team fourth round stage with South Korea hosting Kuwait in the final round of matches in February and Lebanon travelling to the UAE, who have lost all five games.
South Korea had beaten Lebanon 6-0 at home in September but they struggled to establish their normal high-tempo slick passing on the bumpy, hard pitch with the blustery wind also proving a factor.
Without their suspended captain and leading striker Park Chu-young, the Koreans fell behind after five minutes when Ali Al Saadi lashed home an unstoppable drive from six yards after he had blocked his team-mate Roda Antar's shot.
The creative Koo Ja-cheol soon brought the Koreans level from the spot but his clumsy waist-high challenge on Mahmoud El Ali gave away the penalty that resulted in the winning goal, much to the delight of the 40,000 noisy home fans.
