Using rules in conjunction with ontologies is a major challenge for the Semantic Web. This paper propose a novel approach for reasoning with SWRL rules and OWL ontologies based on Predicate Transition net(PrT-net). A feasible method for transforming OWL DL and SWRL rules into PrT-nets is presented. Rule inference is modeled exactly via computing T-invariants of the PrT-net. The main motivation of this work is to provide new insights for computation of T-invariants for rule inference in PrTnet models and to reveal analogies among rule inference and T-invariants methods in Petri net analysis. A small example shows that all the domain knowledge,i.e. the SWRL rule base and the OWL ontology, is required to obtain complete inferences. It illustrates that a whole reasoning model must be provided to interoperate between SWRL and OWL, not only syntactically and semantically, but also inferentially.