Captain Kim Jung-woo headed the Koreans in front in the 10th minute in Tokyo before goals from Koo Ja-cheol, Lee Dong-gook and a superb Lee Seung-yeoul strike made it 4-0 at half-time.
World Cup-bound South Korea took their foot off the accelerator after the break and substitute No Byung-jun completed the rout with a tap-in in injury time.
"I'm delighted with the result and my players," Korean coach Huh Jung-moo told reporters after his side gained a psychological edge over struggling Japan.
"The movement was good and we looked dangerous in attack. A lot of meticulous work goes in on the training ground to produce a display like that. I thank my players for their hard work."
Hosts Japan were fortunate to escape with a goalless draw against China in Saturday's opening game after the away side missed a late penalty.
Huh praised his young side for their attacking play in the absence of Europe-based players such as Manchester United's Park Ji-sung.
"They deserve credit for their work rate and the way they continued to push," he said. "The future looks bright."
Hong Kong's Korean coach Kim Pan-gon also praised the winners.
"Korea's finishing was quality," he said. "Their speed and power gives them an advantage over most teams in Asia."
South Korea face China on Wednesday before meeting fierce rivals Japan at the weekend in the final game of the competition.
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