The 29-year-old Australian took over the #634 Musashi Honda from team-mate Takumi Takahashi just before the end of the first hour, moving into the lead when the Factory Yamaha of Katsuyuki Nakasuga pitted soon after.
Taking part in his first motorcycle race since Valencia 2012, disaster struck for Stoner on the fast, curving, downhill approach to the hairpin. After a front-end wobble, Stoner ran onto the grass where he fell from his CBR1000RR – sending rider and bike somersaulting.
Stoner later revealed that a stuck throttle caused the incident and that he suffered shoulder and leg injuries. Stoner had been able to crawl away, but the Musashi team's hopes of a third straight Suzuka win were well and truly over. A safety car was needed to remove Stoner's battered Honda from the middle of the track.Australian Josh Hook (TSR Honda) then led the race after the restart, before being passed by Nakasuga's team-mate Bradley Smith.
Smith will later hand over to fellow Tech 3 MotoGP rider Pol Espargaro, who qualified the #21 bike on pole, while Stoner would have handed his bike to WSBK star Michael van der Mark.
