Is it possible to force reasoning over an OWL ontology basing on a close world assumption (CWA) in Protégé? Obviously OWL bases on OWA, but I need to close it.
To reason using close world assumption without changing your ontology you need a reasoner that supports that feature. Pellet has an option to use closed world assumption, you will have to check Protégé's settings to make sure it is configurable though.
I'm not aware of other reasoners providing it.
If you cannot use Pellet, you'll have to follow Joshua's suggestion in the comments: modify the ontology to close the world with the right assertions. We can't recommend anything to do that without seeing the ontology, though.