The Asian side took an eighth-minute lead through Kim Jong Eun, and Lee Seon Ok added a second 11 minutes before half-time.
Belgium, the lowest-ranked side in the tournament, got themselves back into the game when Erica Coppey scored just after the interval.
But as they chased a draw late on they withdrew goalkeeper Aisling D'Hooghe to give them an extra outfield player and Korea capitalised as Kim scored her second in the last minute.
Korea will now play Germany, while Belgium will face the USA in the 11th-place play-off as they seek to avoid last spot on their Olympic debut.
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