Kohei Hirate had set the fastest time in Saturday's Q2 pole shootout to take pole in the #24 Nissan Z he shares with Daiki Sasaki.
However, after qualifying it was announced that the Kondo squad has had its times deleted and has been sent to the back of the grid for a violation relating to the capacity of the fuel tank.
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It means that the #36 TOM'S Toyota GR Supra of Sho Tsuboi and Ritomo Miyata will start Sunday's 450km race from pole.
Hirate wrote on Twitter: "It seems the capacity of the fuel tank is over the limit by one plastic bottle's worth, and as a result unfortunately we failed post-qualifying vehicle inspection.
"It's frustrating to lose pole for something not related to the speed of the car, but tomorrow we'll change our mindset and do our best."
Sasaki tweeted: "In qualifying you run with a light tank, so it makes no difference, but it could have been an advantage in the race, so..."
Speaking to Motorsport.com's Japanese edition, Sasaki revealed that the Kondo Nissan was found to be approximately 600cc over the maximum allowed capacity of 100 litres. The capacity of the fuel tank is regulated by the teams through the use of extra 'stuffing'.
He said the sloped nature of the pitlane at Suzuka may have resulted in the team taking an incorrect reading when the tank capacity was initially measured, as taking the measurement on a flat surface could produce a different reading.
"There is no doubt we were quick," he added. "Usually when you think of failing inspection, you think of an engine infraction or ride height infraction. To lose pole for something so trivial is a shame."
Toyota now has a monopoly of the front row with the Racing Project Bandoh machine of Sena Sakaguchi and Yuji Kunimoto starting second ahead of the Team Kunimitsu Honda NSX-GT.
The top Nissan on the grid is now the Team Impul car in fourth.
Additional reporting by Kenichiro Ebii
