Hiroki Otsu was trying to make a move on Ukyo Sasahara for 17th place on lap 4 when the two came to blows at 130R, with both spinning heavily into the barriers.
While Otsu’s Nakajima car had a normal impact with the barriers, Sasahara’s TOM'S machine appeared to fly up into the catch fencing.
Subsequent photo evidence showed the chassis finally came to rest near Degner 1, just before the underpass of Suzuka's famous crossover, with the rear of the car being torn off the car and staying at the 130R barriers.
Otsu was seen walking away from the car in the aftermath of the crash, while Sasahara was reported as conscious and taken to the medical centre for checks.
A safety car was immediately deployed to neutralise the field, before a decision was taken to stop the race altogether, with all remaining cars taking to the grid.
Marshals began work on repairing the barriers, but the scale of the task quickly became clear to the organisers.
After a wait of 30 minutes, it was announced at 3:30pm local time that the race won’t be resumed, with only half points awarded to the top 10 finishers.
With results taken from the end of lap 3 of 31, Nojiri was declared the winner of the race, claiming his third success of the season after previous triumphs at the Fuji opener and Motegi.
Sasahara’s team-mate and championship leader Ritomo Miyata finished second after repassing the Dandelion entry of Kakunoshin Ota at the start of the second lap, having previously slipped behind him with a poor getaway from the front row.
Despite being overtaken by Miyata, third-place for Ota marked his first career podium in Super Formula - and only his second-ever points finish following a sixth-place result at Fuji in July.
Tadasuke Makino was classified fourth in the other Dandelion entry, ahead of Inging rival Sho Tsuboi.
Red Bull junior Liam Lawson had finished fifth on the road after passing Tsuboi at Turn 1 on lap four, but with the final results taken from the end of lap three, Lawson was docked one place, leaving him sixth in the final order.
This was his second-worst finish of the season and followed a disastrous race at Motegi where he collided with team-mate Nojiri and ended up outside the points in 13th.
Lawson had started the race in seventh after a disappointing qualifying session in which he was hamstrung by a lack of fresh tyres, a legacy of his Motegi crash.
Ryo Hirakawa finished seventh for Impul behind Tsuboi, while Kamui Kobayashi (KCMG), Nirei Fukuzumi (ThreeBond) and Ren Sato (Nakajima) completed the points scorers.
Kenta Yamashita and Nobuharu Matsushita, both of whom had started inside the top 10, dropped to 11th and 13th, separated by Yuhi Sekiguchi.
With only Sunday’s finale to run, Miyata holds a 6.5-point lead over defending two-time championship Nojiri, with Lawson slipping 15 behind after scoring only 2.5 points in Saturday’s truncated race.
Race results to follow