Tomato is a significant vegetable crop in India, but it faces substantial losses due to diseases like damping-off (caused by Pythium aphanidermatum) and wilt (caused by Fusarium sp.). To address these issues, a study was conducted to isolate Bacillus sp. from rhizosphere soil to manage the pathogens of P. aphanidermatum and Fusarium sp. Virulent isolates of P. aphanidermatum and Fusarium sp. were isolated from infected tomato plants and were identified morphologically and molecularly as P. aphanidermatum and Fusarium oxysporum. A total of 12 Bacillus sp. were isolated from the rhizosphere soil of tomato field. In vitro, a screening of the Bacillus isolates against the damping-off and wilt pathogens revealed that strains BS1, BS2, and BS5 were effective against P. aphanidermatum, while BS1, BS4, BS7, BS9, and BS11 were effective against F. oxysporum. Notably, strain BS1 was effective against both P. aphanidermatum and F. oxysporum. Volatile GC-MS analysis of the crude extract from Bacillus sp. BS1 revealed the presence of several antimicrobial compounds, including hexanone, benzoic acid, methyl butanol, furan, proline, xylene, dodecane, benserazide, pentanoic acid, and cartap, all with significant area percentages. The result of the volatile analysis showed that benzoic acid was predominantly expressed at high peak values with a higher area percentage (79.2 %), which was found to suppress the pathogenic growth in vitro. A glasshouse trial assessing the efficacy of Bacillus sp. (BS1) demonstrated that treating tomato seeds with 5 g/kg as a basal application and applying 2.0 kg/ha to the soil as a top dressing on days 25 and 35 after sowing resulted in substantial reductions in damping-off (1.29%) and wilt (5.26%) pathogen incidences. Furthermore, the bipartite interaction of plant-defense-related enzymes such as peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, and total phenol content potentially expressed higher activities. This study concluded that Bacillus sp. from the tomato rhizosphere soil exhibits significant potential to inhibit soil-borne plant pathogens.