The Australian has missed the last three races after he fractured his right ankle in a qualifying accident at Indianapolis.
The Honda rider had already said he would be not miss his home race in Australia, but on Wednesday said he will rejoin his team for the Motegi weekend.
"It's been another quiet week here in Australia, I've been resting, having some physio and following doctor's orders to recover," Stoner wrote in his blog on Repsol's website.
"The good news is that I feel I can race in Motegi and will be rejoining my team next week and I can't wait to get back on track.
"I look forward to return in Motegi in front of all the Honda home fans."
Stoner, who has scored four wins this year, is still third in the championship despite his absence, although his chances of retaining the title are mathematically over.
The Australian is retiring from MotoGP at the end of the season.