Yamamoto suffered a major impact with the barriers in the sixth round of the SUPER GT season at Sugo after the Team Kunimitsu driver collided with the Kondo Racing Nissan GT300 car of Teppei Natori.
The two-time GT500 champion was airlifted to hospital in the nearby city of Sendai, and while he was released the same day he was transferred to a different medical facility for further examination.
Team Kunimitsu announced on Tuesday that Yamamoto has been diagnosed with a atlantoaxial subluxation - a misalignment of the first and second vertebrae - and a damaged 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.
Kimura had been registered as the third driver for the #8 ARTA Honda squad for the August Fuji race, but ended up not participating in qualifying or the race as team regular Toshiki Oyu made a full recovery from a broken collarbone.
Team Kunimitsu team director Kazuhiro Kojima commented: "This was a painful decision for [Yamamoto]. Now all we can do is wait for him to return to full fitness and drive our car. We'll support him as much as we can to be able to do this.
"In his absence, Iori Kimura will participate for us. We will do everything we can so that Makino can win the championship, so we ask for your continued support."
In Super Formula, Hiroki Otsu will deputise for Yamamoto for next month's two Suzuka races at Nakajima Racing.
Yamamoto wrote on his Instagram page: "I was shocked when I was forced to make this decision. I'm sorry for the inconvenience caused to all those involved for my withdrawal, and to the fans who have supported me and have been worrying about me.
"I'm still in a situation where I can't shake my anxiety about the future, but I will try to put those feelings behind me and face up to this difficult situation without giving up so that I can definitely make a full recovery!
"I will update on you on the progress of my recovery. I will definitely be back."
Otsu will make his third race outing of the year after he stood in for Tomoki Nojiri at Team Mugen for the Autopolis round in May, and then Oyu and TGM Grand Prix at Fuji in July.
Previously, Otsu participated in the final round of the 2020 Super Formula season for Nakajima when regular driver Makino was unable to participate due to a bout of meningitis.
