The win was 2012 series champ Nakajima’s first of 2014, and sees the former Williams F1 driver move ahead of team-mate and sportscar rival Andre Lotterer in the standings.
Loic Duval, who had led the championship ahead of the Fuji event, was absent following his terrifying crash in practice for last month’s Le Mans 24 Hours. The Frenchman has slipped to third in the standings, with no word on when he will return to Super Formula duty.
He was replaced by Italian Andrea Caldarelli, who duly assumed super-sub status by claiming pole, beating Joao Paulo de Oliveira by less than a tenth of a second. They led a Toyota-powered sweep of the top-six, with Petronas Team TOM'S drivers Nakajima and Lotterer taking the start from fourth and sixth respectively.
However Caldarelli could not maintain his heroics in the race, as rain served to scupper both him and fellow front-row man De Oliveira. The Brazilian had dominated until heavy rain began to fall in the latter stages, and a mistake cost him dearly. Meanwhile Nakajima, Ryo Hirakawa and Yuji Kunimoto all made a quick stop for wet tyres when the safety car was deployed, promoting them to the front.
Hirakawa now led and looked set for his maiden series win, but a final-lap mistake allowed Nakajima to pounce and grab victory. The 20-year-old still claimed his first Super Formula podium, taking the chequered flag within striking distance of Nakajima. Kunimoto completed the rostrum, with Hiroaki Ishiura fourth and Naoki Yamamoto fifth.
Three-time Le Mans winner Lotterer had a disappointing outing. Having looked set to fight for the win the rain scuppered his chance and he could only manage sixth. The German now trails Nakajima by 3.5 points.
Meanwhile former F1 driver Narain Karthikeyan had a solid afternoon in seventh, but Tonio Liuzzi registered his first DNF of the season.
The series is back in action at Motegi on August 24.