The Australian shocked the sport when he announced in May that 2012 would be his final season.
At the time he was in contention for a third championship crown, only for his hopes to be scuppered by a qualifying fall at Indianapolis which left him needing surgery and forced him to miss the following three races.
Having said his impending retirement would only sink in the Monday after Valencia, the 27-year-old admitted the terrible weekend weather and crazy race had made for a bizarre farewell race.
He finished third after a late charge, adding a podium to the sixth straight victory he scored on his home track, Phillip Island, a fortnight ago.
"It all feels a bit surreal at the moment," Stoner said. "I suppose there could be a lot worse ways to go out.
"I like riding this track but it was disappointing all weekend, nothing but miserable weather, and it was difficult to live with to be honest.
"I was very nervous and tense in the race, it was very hard to bring home but in the end our hard work paid off, a few riders slipped off and we made the passes count.
"It's a very good feeling to be on the podium after a race [which was] looking very bad for us.
"I owe everybody so much, I just want to say a big thank you to everyone who has supported me and played a part in my career."
Stoner said he could look back with pride on a seven-year career in the premier class which delivered an unmatched 38 wins and two world titles.
"You can always envisage things going a little differently," he told the BBC.
"I would have hoped to have a little more success than we did, [but] considering the years we have had I can safely say I am very proud of my career, what myself and my team have done.
"I think in such a short time we achieved a lot."
Asked how he had changed as a rider between his 2006 debut with LCR Honda and his 2012 finale, he said: "I'd say just believing in myself, my opinion, and having the right people around me.
"I've always been one to want better; I always think I can be better, always think the bike can be set-up better.
"A lot of people take this as a negative with me, that I am always complaining, but for me it's not complaining, it's striving to be better.
"Even this year I am still learning things I have been trying to for learn for so many years and they have just clicked this year and made my riding a lot easier in certain aspects.
"I think we have grown in the right direction and in the right way.
"I now have a family so I think I have taken a whole new direction in life."
Asked about his future, Stoner said he had no concrete plans, adding: "I have a lot of possibilities in the future, but nothing I am willing to decide and stick to now.
"First we want to take some time off and look at our options and see what direction life takes us."