B-Max driver Kimura went into the Motegi round trailing championship leader Hibiki Taira by 10 points, but got his weekend off to the ideal start by winning Saturday's opening race from pole position.
TOM'S driver Taira meanwhile finished fourth, meaning his advantage was cut to just a single point ahead of Sunday's two deciding races.
Kimura doubled up with another straightforward win from pole in the second race of the weekend on Sunday morning, giving him a nine-point advantage for the finale with Taira only managing fifth.
In the final race, Kimura was beaten off the line by B-Max team-mate Togo Suganami, who went on to score victory, but second was enough to wrap up the championship with rival Taira one place behind.
Kimura becomes the first Honda junior to win the title in the Super Formula Lights era, as well as the second for B-Max following Teppei Natori's 2021 triumph.
The Russian-Japanese driver's success in the secondary category is likely to translate into an opportunity to participate in the post-season test for Super Formula at Suzuka, although whether he will land a full-time seat remains in doubt.
Taira meanwhile may face the prospect of a fourth season in Super Formula Lights after finishing runner-up with three wins to his credit.
Kimura's fellow Honda junior Shun Koide was third overall for Toda Racing, having won four times, while Igor Fraga (B-Max) and Enzo Trulli (TOM'S) were fourth and fifth overall respectively.
Fraga has ambitions to move up to Super Formula next season, while Trulli could stay with TOM'S for a second year in Lights.
One-make turbo engine confirmed for 2024
Super Formula Lights has confirmed it will use the new one-make turbo engine developed by TOM'S starting from the 2024 season.
The series revealed back in June that the TGE33, a new three-cylinder, 1.6-litre unit based on the engine from the Toyota GR Yaris road car, was in development, and a chassis fitted with the new engine was tested in practice from the third round of the season at Suzuka onwards.
A statement released by series organisers stated that a "certain level of reliability and performance" with the new engine had been achieved, and that its introduction for the 2024 season had been approved by Japanese national federation JAF.
It added that the running costs of the new engine are expected to be half of those associated with the current generation of normally-aspirated units supplied by TOM'S, Spiess and Tomei.
