An own goal from Justin Hubner 10 minutes before the interval on Friday gave the Japanese the lead before strikes from Takumi Minamino, Hidemasa Morita and Yukinari Sugawara earned the visitors their fourth win in five qualifiers.
The result takes Japan onto 13 points, seven clear of Australia, Saudi Arabia and China, who are all on six points, with Bahrain on five and Indonesia bottom with three.
The first two finishers in the group advance automatically to the 2026 World Cup while the third and fourth-placed nations have to trawl through a further round of qualifiers.
Ragnar Oratmangoen gave the Japanese an early scare, the striker bearing down on goal after a mistake by Koki Machida in the ninth minute but Zion Suzuki came off his line quickly enough to take the sting out of the shot.
But while the vociferous sell-out crowd and the torrential rain ensured Japan experienced an uncomfortable start, Moriyasu's side slowly started to take control.
The Samurai Blue went in front in the 35th minute, Machida playing the ball inside to Morita, whose miscontrolled pass fell into the path of Daichi Kamada before Hubner scored in his own net under pressure from Koki Ogawa.
Five minutes later the lead was doubled when Kaoru Mitoma delivered low pass from the left that Minamino swept into the bottom corner with a fine first-time strike that Maarten Paes had no hope of saving.
The Indonesians gifted Japan their third goal four minutes into the second half when Paes played the ball directly to Morita and the Sporting midfielder slotted the ball through the legs of two defenders to score.
Sugawara then smashed the ball into the roof of the net, beating Paes at his near post with a thumping strike in the 69th minute as the Japanese wrapped up the scoring in style.
