With this, he moved into the lead in the points table, ahead of the final round in India in late November.
There was high drama on the first morning when four of Gill's main rivals, including his MRF team-mate Ole Christian Veiby from Norway, retired on Stage 3, a press note said here.
Gill, who completed both days with no problems, said after the win: "It is been a perfect weekend, getting maximum points. Most importantly I'm back in the championship and the last round is in India, my home country.
"Japan as always is difficult with such high speeds and rough roads, however we had the perfect tyre choice and the perfect car from our team MRF Skoda."
In the second spot was Mpart's Robert Blomberg (co-driver Lars Andersson) in the Mitsubishi Mirage taking his first podium of the season.
The Swedish driver came second after Cusco Racing's Yuyi Sumiyama (co-driver co-driver Takahiro Yasui) in the Skoda R5 was forced to retire in SS12 due to mechanical issues.
Third place in the APRC class went to Fuyuhiko Takahashi (co-driver Mitsuo Nakamura) in the Subaru Impreza. He was fourth overall in Rally Hokkaido, which was run alongside the Japanese Rally Championship.
Returning after Leg 1 retirements were MRF Skoda's Ole Christian Veiby (co-driver Stig Skjarmoen) in his Skoda R5 and Mpart Sport's Sanjay Takale (co-driver Noriko Takeshita) in his Mitsubishi Mirage in Leg 2.
The title fight goes into the final rally of the 2017 season, with the Rally of India to be held from November 24-26.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)