Many diseases in both human and plants are treated with natural compounds derived from medicinal plants and their extract. This study delves into the effects of the total alcoholic extract of Heliotropium arbainense and its subsequent fractions (ether, chloroform, ethyl acetate and water) were studied as potential alternatives and safe tools for combating Clavibacter michiganensis subsp. michiganensis (Cmm) infecting tomato plants. Notably, this study showed that ethyl acetate, ether extracts of H. arbainense demonstrated clear antimicrobial activity against Cmm. Chromatographic techniques were employed to isolate flavonoid-free and glycoside compounds from the most potent fractions. Concurrently, rhizobacteria, specifically Pseudomonas taiwanensis strain Pst1 OP984768 and Bacillus velezensis strain Bv1 OP984765, were identified for their potential roles in promoting plant growth and acting as bioagents against bacterial wilt diseases. In vitro assays and greenhouse experiments were performed to assess the efficacy of these strains in controlling tomato bacterial wilt caused by Cmm. A synergistic approach, combining fresh cultures of both bacterial strains (Pst 1+ Bv1) and the ethyl acetate extract of H. arbainense, was assessed for its impact on disease incidence and severity. The results indicated a significant reduction in disease severity when employing this combination. Based on the findings, a blend of H. arbainense ethanol extract and Pst1 OP984768 strain and Bv1 OP984765 strain emerges as a promising, environmentally sustainable alternative to conventional synthetic bactericides for managing tomato bacterial wilt instigated by C. michiganensis subsp. michiganensis.