Despite several early scares in front of more than 70,000 fans in Jakarta, the Samurai Blue eventually carved open a home team filled with European-born players before teaching them a footballing lesson.
"I’m really happy. It was a really tough environment in a game away from home," said Japan coach Hajime Moriyasu.
"But I think the fact that so many Japanese supporters came to the stadium and so many Japanese people and supporters (back home) sent their thoughts... these helped the players to endure and battle.
"I think Indonesia had one or two big chances, but I think we persevered through difficult situations to our victory."
The first goal came when Crystal Palace’s Daichi Kamada cut past a defender in the 35th minute and squared the ball across goal, with Indonesia’s Justin Hubner being credited with an own goal as he tried to stop striker Koki Ogawa.
That broke more than half an hour of stubborn Indonesian resistance in heavy rain before Japan showed their superiority, doubling their lead just five minutes later when Monaco’s Takumi Minamino smashed in a low shot.
Sporting Lisbon’s Hidemasa Morita capitalized on a mistake by Indonesian goalkeeper Maarten Paes before substitute Yukinari Sugawara smashed in a fourth to seal the thumping.
Japan are now at the top of Group C by seven points at the halfway stage of the third round of Asian qualifying for 2026, all but guaranteeing them a World Cup berth bar an astonishing collapse.
They will go away to China on Nov. 19 knowing that another win would almost cement their World Cup place, while Indonesia face Saudi Arabia, who have six points with Australia and China.
Just the top two seal their place at the 2026 World Cup in the United States, Canada and Mexico, with the third and fourth forced into another round of Asian qualifying.
Defeat consigned Indonesia to the bottom spot in the group of six, and three points off a coveted top-four spot.
In Group B on Nov. 14, Son Heung-min thanked Tottenham Hotspur for nursing him back to health and said he felt "100 percent" fit after scoring his 50th international goal for South Korea.