Yuji Nakazawa, Yoshito Okubo and Shunsuke Nakamura were on target in rainy Yokohama, relieving the pressure on Japan coach Takeshi Okada following a 1-0 defeat by Bahrain in March.
Japan now have six points from three games in Group Two.
Defender Nakazawa powered home a header to give Japan the lead in the 10th minute before Okubo made it 2-0 with a clinical finish after 21 minutes.
Celtic midfielder Nakamura added a third goal three minutes into the second half drilling a right-footed shot into the bottom corner.