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."
