It was China's first victory over the Koreans since the countries began playing full internationals in 1978.
"I'm delighted with the result," China coach Gao Hongbo told reporters after they moved to four points from two games.
"Our tactics and preparation were spot-on. China are still not at the level of Korea and Japan but we demonstrated excellent mental strength and were fortunate to score three goals."
Yu Hai headed the Chinese in front after just five minutes before Gao Lin pounced on a defensive mistake to rifle home his side's second in the 27th minute in rainy Tokyo.
"We had to lose to China one day," said Korea coach Huh Jung-moo. "It shows how much China have improved. They never let us settle into our rhythm. It was a good wake-up call for us."
South Korea captain Kim Jung-woo's lob was cleared off the line but otherwise China dominated and were rarely threatened.
Huh left with a parting shot for tournament organisers over the decision to appoint a referee from Hong Kong for Wednesday's game.
"I congratulate China on today's win but referees from the same country should not be in charge of matches," he said. "It doesn't help the competition's credibility."
