Stoner claimed 90 points in the five races before Catalunya, but only 60 points in the five races since (although his 14th place at Donington Park was caused by a gamble on wet tyres).
Stoner's place at the Ducati Marlboro team will be taken by rookie Mika Kallio, who will move across from the satellite Pramac squad to ride alongside Nicky Hayden.
Although yet to finish higher than eighth this season, Kallio has been a top six contender at several rounds and already looks set to be retained by Ducati for 2010.
“When I took the call I could hardly believe it, but then I talked to my manager and I realised it was true,” revealed Kallio, who badly injured a finger at Assen. “I am proud to be racing the next three events with the Ducati Marlboro Team.
"Obviously I'm not expecting to suddenly be a second quicker, because our bikes are very similar to the official machines, but I hope to be able to pick up some good results for the team.
"I would particularly like to thank [Pramac boss] Paolo Campinoti, who has allowed me to enjoy this incredible opportunity. It will be a real honour for me. Nonetheless I would like to send my best wishes to Casey, and I hope to see him back out on track as soon as possible.”
Kallio's Pramac seat at Brno, alongside Niccolo Canepa, will be taken by Ducati's factory World Superbike rider Michel Fabrizio. Fabrizio has previously made MotoGP appearances for WCM (2004) and as a stand-in at Gresini Honda (2007).
Fabrizio, who took his first WSBK victory earlier this season at Monza, is currently third in the WSBK championship behind Ben Spies and his team-mate Noriyuki Haga.
The Italian has a previous best MotoGP finish of tenth, which he achieved with both WCM and Gresini.
Stoner's withdraw not only all-but-ends his 2009 title hopes but will also have a massive impact on Ducati, which is heavily reliant on the #27.
The next best Desmosedici rider in the riders' championship is factory team-mate Hayden, in 13th. The American has scored just 47 points compared with 150 for Stoner.