The Welshman led from stage two on Friday morning and never ceased control, beating Sebastien Ogier by 12.8s after 20 stages.
Sami Pajari completed the podium 51.4s away from the lead, while hometown hero Takamoto Katsuta rounded out the all-Toyota top four.
Evans’ second win of the season was also the 50th podium of his WRC career.
“What a great weekend,” said Evans.
“I have to say a huge thanks to the team, amazing car again on tarmac, and thank you to Morizo-san for all your support.
“Hopefully, this win is a token of appreciation.
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“There’s a long way to go in the championship yet. It’s too early to really talk about the title, but we have to just enjoy this win.”
Evans managed long sustained pressure from his teammates, coupled with changing road conditions to hold the lead through every stage following SS1.
Oliver Solberg (Toyota) had reduced Evans’ lead to just 10.6s on the morning of Day 2, however crashed out of the lead battle during that afternoon.
Solberg salvaged crucial points by winning the Power Stage on Sunday afternoon, however finished the rally 21st overall.
Adrien Fourmaux led a Hyundai trio in fifth position ahead of Thierry Neuville in sixth.
New Zealand’s Hayden Paddon finished in seventh place ahead of Jon Armstrong, the first of the Ford Pumas in his Japanese debut.
WRC2 class winner Nikolay Gryazin was ninth outright, with Josh McErlean rounding out the top 10 after a wheel change cost time on Day 3.
Toyota’s dominance in Japan extends its lead in the manufacturers’ standings, now 127 points ahead of Hyundai.
The WRC returns with Acropolis Rally Greece on June 25-28.
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