A system and method for discriminating a fusion beat from an evoked response during the autocapture/autothreshold routines of an implantable stimulation device is provided. The presently disclosed system and method reliably verifies capture in an implantable stimulation device by accurately discriminating a fusion beat from an evoked response based on an analysis and comparison of the morphology, amplitude, polarity, pattern and/or timing intervals of resulting T-waves. The disclosed system for discriminating a fusion beat includes a pulse generator; a means for sensing voltage signals evidencing depolarization and repolarization of cardiac tissue; and a microprocessor based means for determining, based on an analysis of the subsequent T-waves, whether a voltage signal that occurs during the capture detection window is a depolarization voltage signal, which evidences capture, or a fusion beat.