The Musashi Harc Pro team has confirmed that that bike's throttle was stuck 26 percent open, forcing the two-time world champion to crash in the early stages.
The cause of the failure, however, remains a mystery to the squad and the manufacturer, which had been gunning for three consecutive Suzuka wins.
Stoner suffered a broken tibia and scapula in what was a sorry end to his first motorcycle race in almost three years.
“I am really disappointed that the Suzuka 8 hours has ended like this,” Stoner reflected.
“We have done a lot of work over the last few weeks to get accustomed to the bike and the track and work towards a setting that made all of us quite comfortable.
“We really felt that the race and everything had gone as we planned so far, we were very relaxed and comfortable and making sure we saved the tyres and the fuel to stretch the stint as long as we could.
“Unfortunately, we experienced some mechanical trouble as I was going through the corner leading up to the hairpin.
“In this corner I did not have enough time to pull the clutch and have another go at the turn as I came in with too much speed.
“I picked the bike up to try to slow down more but I was heading towards the wall so I decided to lay it over and hit the barrier.
“Unfortunately, they were a lot harder than they looked and we came out of it with a broken bone in the ankle and broken scapula (shoulder blade).”
Despite the drama, Stoner thanked the team for its efforts, which had been good enough to lead at the time of the crash.
“Big thanks to everybody in the team, especially my team mates Michael van der Mark and Takumi Takahashi,” he continued.
“They have done a fantastic job over these weeks and this weekend especially. And I would just like to thank the team for how much effort everybody has put in.
“Their professionalism was outstanding and I really enjoyed working with them. I am very sorry that we could not achieve the strong result I believe we could have.”
Stoner is yet to indicate whether he will return to the event, which was this year won by Honda's arch rivals Yamaha.