The Australian's damaged ankle proved troublesome, compromising his riding style, position and ability to push due. He was seventh fastest in two of the three practice sessions and also in qualifying as a result.
Despite therefore improving during the race, Stoner said his underlying pace - and a start which carried him as high as fourth - proved he could have achieved more.
"I'm a little disappointed, to be honest," he explained.
"We slowly improved over the weekend and got the bike to a point we were pretty happy with in warm up.
"At the start of the race I felt had the pace to stay with Dani and Jorge and the bike was feeling pretty good.
"Then as the race progressed my body started to suffer and ache in ways I didn't expect.
"We had the pace to run a lot higher and be on the podium but unfortunately I couldn't manage it physically today.
"A big thanks to my team, they gave me a fantastic bike today but I couldn't do anymore in my condition."
Stoner will compete this coming weekend at Malaysia before he attempts to defend his crown at his home circuit of Phillip Island in a fortnight's time.
Stoner has won the event for the past five consecutive seasons.