South Korea beat Mexico, 4-3, in pool play, but lost, 3-2, to Team USA in the early stages.
Designated hitter Dae Ho Lee, who drove in the tying and go-ahead runs with a single down the left-field line in the ninth, was named the Player of the Game.
The Koreans were blanked for the first eight innings, thanks to a standout pitching performance from Japan's Shohei Otani. He held South Korea to one hit while striking out 11. Takahiro Norimoto, who was responsible for all four runs and three hits in the ninth, took the loss.
Japan, previously unbeaten in the tournament, climbed out to a 3-0 lead in the bottom of the fourth with a walk, three singles, an error and a sacrifice fly.
After facing the minimum number of batters in seven of the first eight innings, the Japanese ran into trouble in Korea's big ninth inning. Pinch-hitters Jae Won Oh and Ah Seop Son led off with singles before Keun Woo Jeong doubled down the left-field line to get the Koreans on the board.
Yong Kyu Lee was hit by a pitch before Yuki Matsui relieved Norimoto on the mound, but the trouble didn't stop there. Matsui walked Hyun Soo Kim with the bases loaded, plating another run before Hirotoshi Masui relieved him. Then came Lee, whose single turned the game's fortune in the Koreans' favor.
Japan got a single in the ninth, but otherwise went quietly as South Korea advanced.
Joey Nowak is a reporter for MLB.com. Follow him on Twitter at @joeynowak. This story was not subject to the approval of Major League Baseball or its clubs.