The Green Falcons and the Samurai Blue reinstated their three-point lead over Australia in Group B of Asia's World Cup qualifying after Jackson Irvine and Mathew Leckie's goals had seen the Socceroos past the UAE in Sydney.
Gent forward Yuya Kubo and Southampton defender Maya Yoshida completed the scoring in the second half as Japan moved ahead of the Saudis on goal difference.
Saudi Arabia sit second following a 1-0 win over Iraq in Jeddah with Yahya Al Shehri of Al Nassr scoring the winner seven minutes into the second half.
Australia host Saudi Arabia in their next World Cup qualifier in June in a match the Socceroos almost certainly must win to earn an automatic qualifying berth at Russia 2018.
The Socceroos also visit Japan in August and host Thailand in their final Group B fixtures in September.