The Frenchman, chasing a record-equalling ninth title, cut Toyota teammate Elfyn Evans' overall advantage to three points after a wet final leg on the asphalt roads around Aichi and Gifu.
Evans, winner of the past two editions of Rally Japan, finished second, 11.6 seconds behind Ogier.
Toyota's double world champion Kalle Rovanpera finished sixth to remain in contention for a third crown before embarking on a new career in circuit racing.
The Finn is now 24 points off the lead while Hyundai's Ott Tanak no longer has a mathematical chance of the championship after taking fourth place on Sunday. Tanak also announced on Sunday that he would be retiring from the sport after the event in Saudi Arabia.
Evans has 272 points, Ogier 269 and Rovanpera 248. Toyota have already clinched the manufacturers' crown.
"It's obviously a perfect result," said Ogier, who started the season planning only a part-time campaign but can now equal compatriot Sebastien Loeb's record nine titles.
"It has been a challenging weekend because, after this rain today, nothing was certain. Now let's go to the next one."
Hyundai's Adrien Fourmaux, third in Japan overnight, was forced to retire from the race after sliding off into trees.
That left Finland's Sami Pajari in third for his first podium place at the top level, completing Toyota's sweep of the top three in an event based in the manufacturer's home city.
The season-ending round based out of Jeddah over November 26th-29th will be on desert gravel roads, fast at times and rougher terrain at others, and is Saudi Arabia's inaugural World Rally Championship event.