The Australian, a dominant force a fortnight ago at Phillip Island, admitted that he was uncharacteristically tense and nervous throughout the Spanish race, afraid to exacerbate an injury that could still affect him in the future.
Despite that Stoner was still able to seal third following a late charge that he said stemmed from being comfortable enough to push at the close.
"I knew we took the easy way out, I didn't want to take any risks," Stoner reflected.
"I was honestly scared of crashing and injuring my foot any worse, and in these conditions it's the most critical - there were a lot of crashes today.
"I don't feel confident in the wet, I'm constantly tense and not riding like I can, especially in today's conditions.
"Any other time I would have gone to the slick immediately, but something inside me [has been] holding me back and not wanting further injury.
"When we finally went to slick tyres my eyes were the size of dinner plates the whole race, I didn't want to step the front tyre off the dry patch.
"We kept working at it though, trying to improve the speed and in the last couple of laps stood on the blocks.
"It was fantastic really to end [with third] considering how things were looking before the start."
Stoner's third-place means he retires with a victory and a podium in his final two MotoGP races.
He has taken 38 victories over his career, a total unmatched by any other rider during the Australian's spell in the premier class.