Reigning Super Formula champion Naoki Yamamoto eased to victory at Sugo, while Dan Ticktum finished a lap down on a day fellow Red Bull junior Lucas Auer secured a podium.
Dandelion's Yamamoto was locked in an indirect battle with Mugen's Tomoki Nojiri for the lead, as the field split into diverging strategies for the 68-lap race.
A pack of drivers led by Yamamoto started on the soft tyres, with the aim of going longer in the first stint before switching to mediums. The other group - led by Nojiri - got rid of their mandatory stop on the opening lap, putting them in clean air and on the faster soft tyre.
Initially, the race appeared to tilt towards Nojiri as he was lapping comfortably quicker than Yamamoto, who was also held up by backmarkers on the short 3.7 km circuit.
But Yamamoto slowly but steadily upped the pace, extending what was a 37-gap to a nearly 50-second advantage by the time he pitted on lap 52.
That allowed the reigning champion to return to the track still in the lead race of the race, 10 seconds clear of his rival Nojiri.
The late-stopping Auer also managed to jump Nojiri, but came under pressure from the Mugen driver soon after his pitstop.
Nojiri attempted a lunge heading into turn 1, but clipped the inside kerb, pitching himself into a spin and getting beached into the gravel.
With Nojiri unable to escape from the run-off area on his own power, the safety car had to be deployed, neutralising the race.
Moments after the SC retreated, reigning Japanese F3 champion Sho Tsuboi spun on his own at the SP corner, necessitating another intervention.
That left a three-lap dash till the flag, with Yamamoto easing to his second victory at Sugo in as many years.
Auer, however, got stuck behind the lapped cars of Ticktum and Kazuya Oshima, allowing Kamui Kobayashi to sneak through and take second.
Third place was still enough for the Red Bull junior to score his first podium in Super Formula - and the first for the new B-Max by Motopark partnership.
Ticktum's tough season continues
Ticktum's torrid start to the Super Formula season continued as he finished a disappointing 15th, just ahead of Formula 2 convert Artem Markelov and Oshima in the list of classified finishers.
Ticktum had qualified on the last row of the grid and was unable to make much headway after getting rid of the slower medium tyre at the end of lap 1.
The British driver passed Markelov on the outside of turn 1 on the 30th lap of the race, and then cleared Oshima shortly after the second safety car period ended.
But the 20-year-old simply didn't have the pace to challenge the top half of the pack, his fastest lap more than a second slower than Auer's.
With three of the seven races complete, Ticktum has just a single point in his tally, courtesy of an eight place finish at Suzuka.