He went down on the approach to the hairpin and broke his left scapula also fracturing his right tibia.
The reigning champions, Musashi Honda team, were forced to retire due to the bike being badly damaged.
Stoner took to Twitter to confirm his injuries to the public.
"Well my #Suzuka8H ended spectacularly!Stuck Throttle = Broken Scapula Fractured Tibia and a few more tweaks. Sucks," Stoner Tweeted.
"Sorry to my team @mickeyvdmark, Takumi Takahashi and the entire crew, they have worked too hard to end it like that. Thank you guys!"
The Australian won the MotoGP World Championship in 2007 and 2011. Many riders including Ben Spies, Andrea Dovizioso and Nicky Hayden, consider Stoner to be the fastest and most talented rider to have ever raced a motorcycle.