Asia's top-ranked side took the lead on 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, slip to third.
Earlier on Thursday, 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.
Goals from Lewis Miller, Craig Goodwin and debutant Nishan Velupillay sealed the win for the hosts, who had gone behind in the 20th minute through Xie Wenneng’s goal.
Australia jumped above Bahrain into third in the group on goal difference, after the 2019 Gulf Cup champions were held to a 2-2 draw at home by Indonesia.
Only the top two in the six-team group secure direct passage to the 2026 World Cup, with the third- and fourth-placed countries facing another qualifying phase.
In Group B, South Korea were not deterred by the absence of captain and superstar Son Heung-min as they won 2-0 against Jordan in Amman to maintain their unbeaten start to the third round.
Son, who sustained an injury last week for Tottenham in the Europa League, did not travel with his national team to Jordan.
But his absence was not keenly felt as South Korea prevailed through goals from Mainz midfielder Lee Jae-sung and Genk forward Oh Hyeon-gyu.
The win, which offered coach Hong Myung-bo some much-needed relief, moved South Korea to seven points from nine in the group.
South Korea are top of the pool on goal difference ahead of current Gulf champions Iraq, who defeated Palestine 1-0 in Basra.
Aymen Hussein got the game’s only goal to move into the top five in Iraq’s all-time scoring charts, with 29 goals.
Meanwhile, Oman stunned Gulf rivals Kuwait 4-0 in Muscat to get off the mark in the group.
In Group A, Uzbekistan held the much-fancied Iran to a goalless draw in Tashkent to lead the standings, with Amir Ghalenoei's side second.
The UAE are third after they were held to a 1-1 draw at home to North Korea in Al Ain.
Rounding off the group, Asian champions Qatar picked up their first win of the third round with a 3-1 victory against Kyrgyzstan in Doha.
Tintin Marquez’s team sit fourth, level with third-placed UAE on four points and three back from Uzbekistan and Iran.