Tsuboi and Kazuya Oshima finished second in the Rookie Racing-entered #14 Toyota GR Supra on the championship's third visit of the year to Fuji, giving them a single-point lead over TOM'S pair Nick Cassidy and Ryo Hirakawa with three races remaining.
In a charging second stint, Tsuboi made passes on the Kunimitsu and ARTA Hondas and then the Toyota of Hirakawa to secure the #14 crew's best result of the year, despite carrying a 64kg weight handicap, including a stage one fuel flow restrictor.
Sho Tsuboi（#14 WAKO'S 4CR GR Supra）
Oshima, who progressed to eighth in the opening stint before pitting on lap 25 of 66 to hand over to Tsuboi, said tyre management was key to the result.
"In qualifying we struggled, but in the race we had quite a well-balanced car that was kind on its tyres, so we thought we could gain ground, but in the end the result was even better than expected," the reigning champion told Motorsport.com.
"This time the fuel restrictor was included and the success handicap was high, so I thought it would be quite difficult, but in the race we could manage the tyres well.
"Having to catch up in the race means qualifying has not been good, so from now on the challenge will be to do better in qualifying. We need to work a bit more."
#14 WAKO'S 4CR GR Supra