The Czech rider sustained the damage in a crash at Indianapolis, and his subsequent races have been hampered by discomfort from it.
He will now undergo surgery on his left shoulder to repair the ligaments and will sit out the remaining five grands prix as a result.
The family Cardion AB team is looking to have a replacement rider on its Aprilia CRT bike by the Aragon round at the end of the month.
Team boss Karel Abraham Sr said the lack of experienced Czech riders meant the substitute would be of a different nationality.
"Our aim is to find a good pilot able to race already in Aragon next week," he said.
"We preferably considered Czech pilots but neither the promoter nor the association recommended them for safety reasons.
"The priorities include a pilot experienced in MotoGP or at least WSBK racing."