Filippo Preziosi will be replaced as general manager of Ducati Corse as part of a wider reorganisation which will come into effect at the start of 2013.
The Italian, who has been at the helm of Ducati's MotoGP project since its 2003 race-winning debut season, will make way for Bernhard Gobmeier, former director of BMW's World Superbike programme.
Preziosi will take up a new role as director of R&D at Ducati Motor Holding.
Alongside that change, Paolo Ciabatti will return to Ducati as the team's MotoGP project director.
The Italian spent a decade helping to run Ducati's WSBK team, when the likes of Carl Fogarty and Troy Bayliss delivered massive success, before moving to WSBK organiser FG Sport.
In his previous role with BMW, Gobmeier said earlier this year that Honda and Yamaha were 'killing' MotoGP by focusing too heavily on technology.
The reorganisation follows Audi's recent acquisition of Ducati and a dearth of on-track success.
The team's last victory came when Casey Stoner won his home grand prix at Phillip Island in late 2010.
Andrea Dovizioso and Nicky Hayden will ride for Ducati's works team next season, with Ben Spies and Andrea Iannone installed at the newly-established Pramac satellite squad.