There are a few external OWL reasoners that work with Apache Jena APIs. The following web pagedescribes a way to use Pellet together with Apache Jena APIs: http://clarkparsia.com/pellet/faq/using-pellet-in-jena/

TrOWL can also be used as a Apache Jena reasoner. Refer to the following page for details: http://trowl.eu/