Stoner returned to racing with Honda in this year's Suzuka eight hours endurance race but crashed when his bike's throttle jammed.
There has been speculation that the 30-year-old, who has also tested for Honda, could make a MotoGP return with Ducati as a wild card but neither the manufacturer nor rider alluded to that on Monday.
"I have so many great memories working with the people and the brand of Ducati and the opportunity to work with them again is something very special," said Stoner in a statement announcing his new role.
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"I'm looking forward to assisting the team, (riders) Andrea Dovizioso and Andrea Iannone however I can."
(Reporting by Alan Baldwin, editing by Ken Ferris)
