Kwon Chang-hoon opened the scoring in the seventh minute for the Asian heavyweight, Northern Ireland equalising by forcing a Kim Min-jae own goal from a clever set-piece 13 minutes later.
Korea Republic, featuring Tottenham Hotspur star Son Heung-min and led by Swansea City midfielder Ki Sung-yueng, controlled possession and pressed in search of a second goal after the break.
But a succession of substitutions as the game wore on interrupted the flow of the contest and Northern Ireland — missing the likes of regular captain Steven Davis and centre-forward Kyle Lafferty with injury and with highly rated young Norwich full back Jamal Lewis making his debut — pounced to snatch victory through debutant Paul Smyth with four minutes remaining.
It was a gratifying and somewhat unexpected outcome for Northern Ireland boss Michael O'Neill, who in January rejected the advances of Scotland as it sought to appoint him as Gordon Strachan's replacement.
Next up for Korea is a friendly against fellow FIFA World Cup participants Poland in Chorzow as it builds toward matches against Sweden, Mexico and holder Germany at the finals in Russia.
Northern Ireland is not back in action until facing Panama in May.