Omega-3 and probiotics were shown to improve periodontal health by modulating the host immune response. Recently, the combination of omega-3 and probiotics has been shown to have a potential synergistic effect on host modulation. The aim of this study was to evaluate the prophylactic role of an omega-3 and probiotic combination on alveolar bone loss (ABL) via inflammatory response in an experimental periodontitis model. Forty-three rats were divided into 5 groups as control (C, n = 8), periodontitis (P, n = 8), omega-3 + periodontitis (O, n = 8), probiotic + periodontitis (Pro, n = 10), and omega-3 + probiotic + periodontitis (OPro, n = 9). Additionally to a standardized diet, omega-3 and/or probiotics were supplemented with oral gavage to the O, Pro, and OPro groups for 44 days. Periodontitis was induced by ligature to the P, O, Pro, and OPro groups on the 30th day for 2 weeks. ABL levels were measured histopathologically, and serum interleukin (IL) 1 beta, IL6, and IL10 levels were analysed by enzyme-linked immunosorbent assay. ABL increased in all periodontitis groups (P, O, Pro, and OPro), compared to C group. Compared to P group, all oral gavage groups (O, Pro, and OPro) revealed decreased ABL, which was lowest in OPro group. IL1 beta and IL6 decreased and IL10 increased in OPro group, compared to P group. In conclusion, prophylactic administration of omega-3 and probiotic combination reduced ABL and improved serum IL1 beta, IL6, and IL10 levels more than their single use.