Miyata, a race winner in both Super Formula and SUPER GT, will partner Takeshi Kimura and Scott Huffaker at the wheel of the CarGuy Racing-branded Kessel Ferrari 488 GTE for Sunday's six-hour race.
The Toyota WEC Challenge driver replaces factory Ferrari racer Daniel Serra, who according to a statement released by CarGuy is unable to travel to Japan due to "various circumstances".
Miyata was due to attend the Fuji race anyway with the Toyota squad, having also been present for the Le Mans 24 Hours and Monza rounds of the WEC as part of his development programme with the Japanese marque.
It will mark Miyata's first outing in GTE machinery, and comes at a time that Toyota is weighing up whether to place him in the WEC next season.
The 24-year-old is already a race winner at Fuji this year, having taken victory alongside Sho Tsuboi for Toyota squad TOM'S in the first of two SUPER GT races to have taken place at the circuit in 2023.
He also leads the Super Formula standings ahead of current AlphaTauri Formula 1 driver Liam Lawson ahead of next month's final round of the season at Suzuka.
Elsewhere on the Fuji GTE Am entry list, Kei Cozzolino and Hiroshi Koizumi will drive for the AF Corse team alongside Simon Mann.
The Japanese duo, who race together in the Michelin Le Mans Cup series, effectively replace Ulysse de Pauw and Julien Piguet, Mann's team-mates aboard the #21 Ferrari at Le Mans and Monza.
It will mark Koizumi's first WEC outing since 2013, while series veteran Cozzolino will be making his second outing of the year after appearing at Le Mans as part of an all-Japanese driver line-up for Kessel together with Naoki Yokomizo and Yorikatsu Tsujiko.
