O JPA 2.1 agora suporta procedimentos armazenados, leia o documento Java aqui .
Exemplo:
StoredProcedureQuery storedProcedure = em.createStoredProcedureQuery("sales_tax");
// set parameters
storedProcedure.registerStoredProcedureParameter("subtotal", Double.class, ParameterMode.IN);
storedProcedure.registerStoredProcedureParameter("tax", Double.class, ParameterMode.OUT);
storedProcedure.setParameter("subtotal", 1f);
// execute SP
storedProcedure.execute();
// get result
Double tax = (Double)storedProcedure.getOutputParameterValue("tax");
Veja o exemplo detalhado aqui .