Objectives The aim of this study was to investigate the cellular changes caused by Bisphenol A (BPA) exposure in salivary gland cells and to examine the protective role of resveratrol (RSV) and apigenin (APG) molecules against the negative effects of BPA. Materials and Methods Forty-two rats were randomly divided into 6 groups as; (i) control, (ii) BPA (130 mg/kg), (iii) BPA + RSV100 (100 mg/kg), (iv) BPA + RSV200 (200 mg/kg), (v) BPA + APG100 (100 mg/kg), and (vi) BPA + APG200 (200 mg/kg). In all experimental groups, the chemicals were given by gavage every day for a total of 28 days. Results The BPA administration caused a significant increase in tissue oxidative stress parameters as opposed to a significant decrease in tissue antioxidant levels (p < 0.05). On the other hand, it was observed that RSV and APG treatment reversed this situation (p < 0.05). The BPA administration did not cause a significant change in tissue prostaglandin E-2 (PGE(2)) and nitric oxide levels, whereas low-dose RSV significantly reduced the tissue PGE(2) levels compared to BPA (p < 0.05). BPA caused cytopathological changes and apoptosis in salivary gland cells. In the BPA group, edema, nuclear pleomorphism, and pyknotic nuclei were observed. Moreover, both RSV and APG were found to provide protection against BPA-induced cellular damage, while RSV provided better cellular protection than APG. The control group had a normal histological structure. Conclusion BPA caused cytopathological changes and apoptosis in salivary gland cells. As a result, it was observed that these phytochemicals probably have cytoprotective effects in BPA intoxication.