Nakayama brought home SARD's Toyota GR Supra for a first victory for himself and Heikki Kovalainen since last year's Autopolis race by a margin of 10 seconds.
The decisive moment of the race came when poleman Nirei Fukuzumi in the ARTA Honda NSX-GT and Kovalainen pitted together on lap 26, after which Tomoki Nojiri struggled badly on his out lap in the ARTA car and was passed for the net lead by Nakayama.
#39 DENSO KOBELCO SARD GR Supra
Kovalainen was pessimistic of his chances of a top result at Fuji speaking to Motorsport.com ahead of qualifying on Saturday, saying the gap to the TOM'S and Cerumo Toyotas that were carrying more success ballast was too small.
But the ex-Formula 1 racer said that the car felt better on Sunday morning ahead of the race and he knew that a strong result could be in the offing.
"Already in warm-up the car felt good," the Finn told Motorsport.com. "We had the tyres from practice and they felt good. I thought there was a chance, the win was unexpected, but once I got going, it looked like we had a chance and it all worked out."
On his stint, he said: "I was trying to catch the cars in front, but the gap wasn’t coming down so I tried to save some fuel and trying to make the fuelling time shorter. It worked out well, the pitstop was fast, and [Nakayama's] out lap was really good.
"After that I knew he can control the situation, he did the same at Autopolis last year. So once he got the five second gap [over second place], I knew he was saving something for later and that he had the pace to bring it home."
Additional reporting by Ryo Harada
Yuichi Nakayama, Heikki Kovalainen（#39 DENSO KOBELCO SARD GR Supra）