Asia's top-ranked side took the lead in 14 minutes in front of more than 56,000 fans at King Abdullah Sports City, when Crystal Palace midfielder Daichi Kamada finished from close range following good work from Brighton's Kaoru Mitoma.
Japan then made the result safe eight minutes from time, substitute Koki Ogawa heading home Junya Ito's corner. The victory lifts Japan, who have qualified for the past seven World Cup finals, to nine points from three games in Group C.
They host Australia in Saitama on Tuesday. Saudi Arabia, managed by the under-fire Roberto Mancini, slipped to third. Earlier, the Socceroos came from behind to defeat China 3-1 and resurrect their qualifying campaign to ensure Tony Popovic's reign as coach got off to a winning start.