Shinji Kagawa scored two goals for the Japanese, first in the 35th minute and then in the 53rd. It was the Borussia Dortmund striker's first match for Japan since breaking a bone in his right foot in January at the Asian Cup in Qatar.
Keisuke Honda also scored for Japan, making it 2-0 in the 51st.
The Japanese controlled the ball for the majority of the game at Sapporo Dome with South Korea struggling to mount much of an attack in the final warmup match for both nations before World Cup qualifying begins in September.
Kagawa put Japan in the lead with a shot from just outside the box. Yasuhito Endo stole the ball and directed it to Tadanari Lee, who sent a nifty back-heel pass to Kagawa. The striker then beat South Korea goalkeeper Jung Sung Ryong with two defenders all over him.
Honda doubled the advantage early in the second half after being fed by Hiroshi Kiyotake, who controlled a deflection by Jung off a shot from Tomoaki Makino.
Kagawa scored his second goal with a clinical finish only two minutes later, executing a give-and-go with Kiyotake.
Lee, a fourth-generation South Korean born in Tokyo who became a Japanese citizen in 2007, started for Japan in his first match against his ancestral homeland.
The teams last met at the Asian Cup, where Japan beat South Korea in the semifinals and went on to win its fourth continental title by defeating Australia 1-0 after extra time.
Japan wore black armbands in memory of former international Naoki Matsuda, who died last Thursday at the age of 34, two days after suffering a heart attack and collapsing during training with his Japan Football League club.