Second-half goals from Daichi Kamada and Takefusa Kubo ensured the Samurai Blue secured a spot in Asian group C's top-two automatic qualification places on Thursday.
Crystal Palace midfielder Kamada came off the bench to put Japan in front in the 66th minute and Kubo added the second three minutes from time.
Their sixth victory from seven matches means Japan, who will be in an eighth successive finals, qualify for the expanded 48-team tournament, joining co-hosts, the United States, Canada and Mexico.
After an underwhelming first half, coach Hajime Moriyasu introduced Kamada in the 63rd minute and, within three minutes, he had put his side in front.
The 28-year-old finished off a fine move that started with defender Hiroki Ito finding Ayase Ueda in the centre circle, and his pass released Kubo to set up Kamada to score.
Kubo had been Japan's most potent threat and it was fitting that the Real Sociedad playmaker added the second, beating goalkeeper Ebrahim Lutfallah at his near post to put the outcome beyond doubt.
The result means Japan continue to lead group C by nine points from second-placed Australia, who overcame an early scare to thrash Indonesia 5-1 in Sydney, with the help of two goals from Jackson Irvine.
The top two from each of the three six-team groups in the third round of Asian qualifying advance to the World Cup while the third- and fourth-placed teams advance to another stage to compete for two more places.
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