The game marked the fourth meeting between the two teams in World Baseball Classic play this year. The countries have won two games each.
It was a tuneup for this weekend's games.
"Today, we didn't put great meaning to winning or losing," Korea manager In Sik Kim said. "Today, I thought there were some players who didn't play the game. We were saving some of the players that pitched in the winning games."
Tied at 2 in the top of the eighth, Japanese pinch-hitter Michihiro Ogasawara replaced left fielder Seiichi Uchikawa and drove home Norichika Aoki with a single to right field to push his team ahead, 3-2. Japan scored three more times to extend the lead to four runs to seal the victory.
As for Korea, the offense went to work on Japan left-hander Tetsuya Utsumi in the first inning.
Second baseman Keun-Woo Jeong led off the bottom of the inning with a single and advanced to second base when the next hitter, right fielder Yong-Kyu Lee, dropped a sacrifice bunt. Jeong scooted home on a ground-rule double by the third hitter, Hyun-Soo Kim, and just like that, Korea had a 1-0 lead.
In the second inning, Japan answered with a home run by Uchikawa off Korea starter Wonsam Jang to tie the game at 1. First baseman Shuichi Murata followed with a single and advanced to second base on an error by Korean center fielder Taek-Keun Lee.
Murata moved to third on a single by second baseman Akinori Iwamura and scored on a base hit to right field by Yasuyuki Kataoka to push Japan ahead, 2-1.
Korea received a scare in the bottom of the third inning when Yong-Kyu Lee was hit by a pitch in the back of the head by Utsumi. Play was halted while Lee, writhing in the batter's box, was checked out by the Korean staff. He eventually stood up and trotted to first base before being replaced by pinch-runner Jong Wook Lee.
Japan did not leave the field unscathed. In the top of the fourth, Murata picked up his second hit of the game, this time a single to center field, but injured his hamstring running to first base. He was removed from the game and replaced by pinch-runner Yoshiyuki Kamei. Murata's injury was so severe that after the game the Japanese began a petition to replace him on the roster with Hiroshima Toyo Carp infielder Kenta Kurihara.
"We have other important games left and he has to be replaced," Japan manager Tatsunori Hara said.
In the bottom of the seventh, Bum Ho Lee's solo home run over the 396-foot marking in center field tied the game at 2. The home run was Lee's second of the tournament.
As for Jang, he was charged with five hits and two runs in three innings. He threw 45 pitches.