The aim of this study was to investigate the effect of dental caries on the stability of the periodontal system. This study presents a numerical analysis performed with three-dimensional (3D) finite element (FE) method to evaluate stresses in the bone surrounding the tooth with dynamic mastication combined loadings. In this work, we present a comparative study on infected and healthy periodontal systems. The infected tooth was modeled and a caries defect was introduced to the tooth coronal part. The infected tooth was evaluated and equivalent von Mises interface stress values were obtained for comparison with the ones exhibited by the healthy tooth. Our results by 3D FE analysis indicated that maximum stresses occurred primarily at the cervical level of root and alveolar bone. In the cortical bone, the stress value was greater in infected system (21.641 MPa) than in healthy system (15.752 MPa), i.e., a 37.4% increase. However, in the trabecular bone we observed only 1.6% increase in the equivalent stress values for the infected tooth model. Stress concentration at the cervical level may cause abnormal bone remodeling or bone loss, resulting loss of tooth attachment or bone damage. Our findings showed that decayed single-rooted teeth are more vulnerable to apical root resorption than healthy teeth. The numerical method presented in this study not only can aid the elucidation of the biomechanics of teeth infected by caries but also can be implemented to investigate the effectiveness of new advanced restorative materials and protocols.