“My team are like my second family, we've been through a lot of ups and downs together and it's going to be difficult not to see them every week though.
“I'm sorry for them and for everyone who has supported me for so long but this is the way it is and it's time to say goodbye. Thank you to all the people who have supported us over the years and all our sponsors, and to everyone in the Repsol Honda Team".
Stoner became Ducati's only world champion at his first attempt in 2007 and left the factory with 23 wins at the end of 2010.
To date, only one other Ducati rider has won a race since 2007 - a wet/dry victory for Loris Capirossi - but Stoner's talent only became truly appreciated when his replacement, seven-time MotoGP champion Valentino Rossi, took just three podiums in 35 starts.
By contrast, Stoner clinched his second title in his first season with the factory Honda team, matching his 2007 tally of ten wins from a record-equalling 16 podiums. Stoner scored a further five wins this season, to finish third in the world championship.
On completion of his final MotoGP race, Stoner was named as an official 'MotoGP Legend'.
He becomes the 20th person to receive the honour, alongside: Giacomo Agostini, Mick Doohan, Geoff Duke, Wayne Gardner, Mike Hailwood, Daijiro Kato, Eddie Lawson, Anton Mang, Angel Nieto, Wayne Rainey, Phil Read, Jim Redman, Kenny Roberts, Jarno Saarinen, Kevin Schwantz, Barry Sheene, Freddie Spencer, John Surtees and Carlo Ubbiali.
Stoner has been linked with a switch to V8 Supercars, but insists he has no fixed plans for the future.