Kondo Racing Nissan GT300 driver Natori made contact with Yamamoto's Team Kunimitsu Honda NSX-GT while trying to enter the pits exiting the final corner on lap 37 of 84, sending Yamamoto into the barriers at high speed.
The incident led to the race to be red-flagged, although it later resumed, while Yamamoto was airlifted to hospital.
On social media, Natori wrote: "I'm very sorry to Yamamoto, the #100 [Kunimitsu] team and all those involved, as well as fans of the #100 car, for the contact in this race that caused this situation.
"I will endeavour to make sure this kind of contact doesn't happen again."
Honda subsequently reported that Yamamoto had escaped major injury following his examination at hospital.
The Kondo Nissan GT-R NISMO GT3 of Natori and Joao Paulo de Oliveira was handed a drive-through penalty for causing the collision, and then was given a second drive-through as de Oliveira had been judged to have illegally touched the car during the red flag period.
De Oliveira recovered to finish 11th on the road, but he and Natori were promoted to the final points-paying position in 10th when the class-winning Team UpGarage Honda NSX GT3 was disqualified post-race.
How the crash unfolded
While the accident involving Yamamoto was never shown on TV, fan footage captured from the outside of the last corner, looking up the hill towards the pit entrance, shows clearly how it happened.
Natori was battling the #10 Gainer Nissan when he appeared to slow and move across the track to the right to enter the pits, only to check up because the Rookie Racing Toyota GT500 car of Kenta Yamashita had committed to passing him on the right.
Yamamoto was running close behind Yamashita in the slipstream and followed the same path, most likely unaware Natori was trying to pit.
In turn, Natori would have most likely not seen that Yamamoto was tucked into Yamashita's slipstream - and so he veers right so as not to miss the pit entrance as soon as the Rookie car clears him, only to make contact with Yamamoto.
The contact will inevitably raise questions over whether the layout of the pit entrance at Sugo could be improved to avoid similar incidents in future.
Some in the paddock have suggested that the white line could be extended further towards the final corner so as to force cars that are pitting in to hold a tight inside line through the long right-hander.
Additional reporting by Kenichiro Ebii
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