Ducati privateer Karel Abraham and his Cardion AB team will switch to MotoGP's CRT class next season and run an Aprilia.
Abraham has used a satellite Ducati since moving up from Moto2 in 2011.
But after an encouraging rookie season, the Czech rider has become frustrated during an injury-blighted 2012 campaign.
Cardion's technical chief Luigi Dall'Igna said the team had rejected a chance to continue with Ducati, which has instead restructured its relationship with fellow satellite squad Pramac for 2013.
"In spite of the fact that we had the option to continue with Ducati in 2013, we decided not to use it, and to give an opportunity to a new partner," said Dall'Igna.
Abraham believes the move to CRT and Aprilia will be good for his career.
"The 2012 season has regrettably been a step backwards," he said.
"It's a pity that we are finishing our co-operation with Ducati in these circumstances, but this year things haven't been working as well as they should.
"We have been in negotiation with Aprilia for quite some time, and I think the partnership's got a good future. I see it as the best possible solution.
"It's going to be a lot of hard work, but we think it's important to be going forward and not just running on the spot."
- Karel Abraham