Following a minute's silence in memory of Matsuda before kick-off in Sapporo, midfielder Shinji Kagawa put the Blue Samurai in front with a sharp right-foot finish after 34 minutes.
Keisuke Honda made it 2-0 eight minutes into the second half, clinically firing a left-foot shot just inside the post before Kagawa grabbed his second from point-blank range moments later following a flowing move from Japan.
Japan's players, unbeaten in 11 matches under Italian Alberto Zaccheroni and wearing black armbands, pointed skywards in tribute to Matsuda, who died last Thursday aged 34, after each goal in a rare win over the Koreans.
"We played with passion from the start and never lost our focus," Zaccheroni told reporters after Japan had beaten South Korea at home for the first time since 1998.
"To beat a quality side like South Korea with this kind of performandce gives us a confidence boost ahead of the World Cup qualifiers."
Both sides were using the game as a warm-up for the third round of Asian 2014 World Cup qualifiers which begin on September 2.
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