Yamamoto suffered a major impact with the barriers at Sugo after he collided with the Kondo Racing Nissan GT300 car of Teppei Natori.
The two-time GT500 champion was airlifted to hospital, and while he was released the same day he was transferred to a different medical facility for further examination.
Honda announced on Tuesday that Yamamoto has been diagnosed with a damaged vertebra and spinal cord in the wake of his accident.
It means he will miss the final two rounds of the SUPER GT season at Autopolis and Motegi, as well as the final Super Formula double-header at Suzuka.
Yamamoto will be replaced by Honda reserve Iori Kimura alongside Tadasuke Makino in the Team Kunimitsu Honda NSX-GT for the final two SUPER GT races.
In Super Formula, Hiroki Otsu will deputise for Yamamoto for the Suzuka races at Nakajima Racing.
More to follow
