The Australian told local media on Monday he wanted to race at his home grand prix on Oct. 28 before retiring in November.
Stoner, who expects to be sidelined for up to seven weeks following surgery, said: "Being at Phillip Island is definitely my goal at the moment."
The Honda rider, third behind Spaniards Jorge Lorenzo (Yamama) and Dani Pedrosa (Honda) in the title standings, ruled out racing next year to try to end his career on a high.
"I'm not in this championship to wait and finish it perfectly in a big fairytale," he said. "I'm not racing next year.
"I could have a similar issue and something else could go wrong. I still have a season to complete, I want to get back to racing as soon as possible."
Stoner added that he would like to squeeze in one race before Phillip Island -- the Malaysian Grand Prix on Oct. 21.
"As long as I can't cause any more damage, then I'll have a go," the 26-year-old told Australia's AAP news agency.
"I don't really care about pain but if there is any chance of doing huge damage then there is no point.
"I'm definitely planning to be fit and ready for the Island," added Stoner, who won the first of his two MotoGP world titles with Ducati in 2007.
"It is the one race I don't want to miss. Until I have the surgery I can't say exactly when I can return."
Stoner was ruled out of Sunday's Czech Grand Prix, won by Pedrosa, after a high speed fall in practice at Indianapolis the previous week.