Evans sealed his eighth career win when he finished one minute and 17.7 seconds ahead of French part-time teammate Sebastien Ogier (39), with double world champion Kalle Rovanpera (23) third.
Finland's Rovanpera had already clinched the title with a round to spare last month, and Japan's result confirmed Evans as championship runner-up.
Toyota were already crowned manufacturers' champions for the third year in a row.
"It’s really nice to be on the top step of the podium again and even more so when it’s a one-two-three for the team," said Evans, overall runner-up for the third time in his career.
"We could not have asked for a much better event at home for Toyota.
"On Friday we had exceptionally tough conditions which we came out of with quite a margin. Since then it’s been a challenge in a different way, trying to manage the gap rather than push flat-out, but I’m very happy to get there in the end."
Evans had led by nearly two minutes after Friday's wet opening leg on the asphalt stages and could then control the pace.
Hyundai's Esapekka Lappi (32) took fourth place to deny Toyota an even greater sweep, with Japanese driver Takamoto Katsuta (30) finishing fifth for the champions after winning nine of the 21 stages but losing time in a Friday incident.
Estonian Ott Tanak (36) was sixth in his last outing for M-Sport Ford before returning to Hyundai next season.
The 2024 season starts in Monte Carlo on January 25th-28th.
