With rain hitting the former Pacific Grand Prix venue as expected on Sunday afternoon, the start was delayed by an hour and race itself was shortened to 70 minutes.
However, the rain refused to ease off, forcing the organisers to bring out the red flags after just seven laps under the safety car.
A 45-minute lull followed before the race began in earnest, with Kobayashi immediately pressuring polesitter Sekiguchi as the two broke away from rest of the field.
Kobayashi slammed into the back of Sekiguchi at the hairpin and then slipped past him in the following corner to seize the lead.
Despite that contact leaving Kobayashi’s car with nose damage, the Toyota LMP1 star managed to continue, building a seven-second lead in just a few laps.
However, his advantage was nullified when the safety car was called in again after Nirei Fukuzumi and Tom Dillmann went off at the final corner as Dillmann dived down the inside.
Fukuzumi managed to resume after losing a few places, but Dillmann had to retire, with his car’s front wing left in a dangerous position on track.
At the restart, Kobayashi was quick off the mark but made a mistake heading into the double hairpin, running wide and handing the lead back to Sekiguchi.
He managed to claw his way on to the tail of Sekiguchi again, but before he could make a move the safety car had to be called again, this time for a spin involving Fukuzumi.
With just four minutes on clock, the race finished under the safety car, with Sekiguchi winning the race from Kobayashi and Ryo Hirakawa making it two Impul cars on the podium.
Tomoki Nojiri was the only Honda points-scorer in fourth, while Nick Cassidy extended his lead in the championship with a fifth-place result.
Kenta Yamashita was classified sixth ahead of Hiroaki Ishiura, who managed to pass his teammate Yuji Kunimoto right before the penultimate caution period to take seventh and rise up to second in the drivers’ standings.
Nobuharu Matsushita and Naoki Yamamoto completed the top 10.
With less than 75 percent of the race distance completed, only half points were awarded. Cassidy holds a four-point advantage over Ishiura heading into the Suzuka finale, with Yamamoto a point adrift in third.