By the 33rd lap the No.23 Motul Autech GT-R was in the lead again, but contrary to the team's prediction, the rain never reached the main track. This made things hard for Motoyama on his deep-groove tires as the track continued to dry out. On the Dunlop Corner of lap 43 Motoyama was finally passed by the No.1 Weider HSV-010 driven by Takashi Kogure running on shallow-groove tires. Soon after that, however, the No.100 Raybrig HSV-010 of Naoki Yamamoto crashed on the 200R turn, bringing out the Safety Car.
After the race was restarted on lap 46 with the cars' tires now cool and grip poor, Motoyama in the No.23 Motul Autech GT-R continued valiantly to try to hold onto second place, but that effort ended when he ran off the track on lap 50. This allowed Kazuki Nakajima in the No.36 PETRONAS TOM'S SC430 and Takuto Iguchi in the No.39 Denso SARD SC430 to move into second and third positions respectively.
Running in the lead, the No.1 Weider HSV-010 was hit unexpectedly by a GT300 car on the chicane of lap 53 and spun out as a result. This allowed the No.36 PETRONAS TOM'S SC430 to move up into the lead position.
By this point in the race, the track was getting even drier, and when the No.24 Advan KONDO GT-R of Bjorn Wirdheim made its second pit spot on lap 60 and changed to slick tires, Ronnie Quintarelli in the No.46 S Road MOLA GT-R and Kazuya Oshima in the No.6 ENEOS Sustina SC430 followed suit and changed to slicks as well.
However, with about 20 laps remaining in the race the rain began to fall lightly again, causing Loic Duval in the No.1 Weider HSV-010 and Juichi Wakisaka in the No.35 D'STATION KeePer SC430 to choose shallow-groove tires. These turned out to be the decisions that would determined the outcome of the race.
In the final stages of the race, the No.46 S Road MOLA GT-R of Quintarelli running on slick tires ran a succession of fastest laps of the race in a blazing charge that moved it into second position just 1.8 sec. behind the leading No.1 Weider HSV-010. Then the rain began to fall again, turning the advantage once again to the No.1 Weider HSV-010 and helping it on to its second win of the season. The No.46 S Road MOLA GT-R finished second with the No.12 Calsonic IMPUL GT-R coming home third.