Yuya Osako buried a first-half penalty to put the four-time Asian champions in control in Saitama, north of Tokyo, before Junya Ito doubled their lead after the break.
The win meant Japan stayed second in Group B behind leaders Saudi Arabia, who they host at the same stadium next Tuesday in a crucial clash.
With Australia just a point behind Japan, three teams are battling it out for two automatic spots in Qatar as the qualifying campaign approaches its conclusion.
“Looking ahead to the Saudi game, tonight’s match has helped strengthen our understanding as a team and that’s a big plus for us,” said Japan manager Hajime Moriyasu.
“But the Saudi game will have a different intensity and tension from tonight, and we have to be ready to play at a high level.”
Australia stayed in the hunt for an automatic berth with a comfortable 4-0 home win over Vietnam.
Jamie McLaren opened the scoring in the 30th minute in Melbourne before Tom Rogic notched a second in first-half injury time.
Craig Goodwin and Riley McGree added two more after the break to wrap up the win for the home side, whose manager Graham Arnold was absent after testing positive for Covid-19.
Japan were missing half their regular defence against China, with captain Maya Yoshida and Arsenal full-back Takehiro Tomiyasu both missing through injury.
But the home side took a 13th-minute lead after China defender Wang Shenchao slid in to block Ito’s cross but hit the ball with his arm.
Osako made no mistake from the spot and the hosts pressed home their advantage in the 61st minute when Ito rose to head home substitute Yuta Nakayama’s cross.
“We had a mix of overseas and domestic-based players so they were all at different levels of fitness,” said Moriyasu.
“But despite that they combined well and communicated well and did a good job.”
China, who were playing their first game under new manager Li Xiaopeng, saw their slim hopes of reaching the World Cup all but ended.
“The players gave their all but the first goal came at a bad time for us and it threw us out of our rhythm,” said Li.
“It had a really big impact.”