Efficient and sustainable food production is crucial in global agricultural development. Overuse of chemical fertilizers leads to soil acidification, destruction of soil properties, and harm to soil micro-organisms. Plant growth-promoting rhizobacteria (PGPR) have emerged as a solution, enhancing soil fertility and crop yields while reducing chemical fertilizer dependency and disease occurrence. In this study, Bacillus strains KHC2, KHH5, and KHH13, isolated from organic rice field soils in Taiwan, were identified through molecular techniques as B. velezensis (KHC2, KHH13) and B. amyloliquefaciens (KHH5). The strains exhibited various hydrolytic enzymes (including protease, cellulase, amylase, and lecithinase), with KHH13 showing the highest phosphate solubilization (2186.1 µg mL−1 day−1) and indole-3-acetic acid (IAA) production (63.067 ± 0.595 ppm mL−1). These properties indicate KHH13’s potential as a bio-enhancer for plant growth. Therefore, we hypothesized that KHH13 can enhance plant growth and control soil-borne diseases. A greenhouse experiment demonstrated that KHH13, KHC2, and KHH5 effectively promoted the growth of red lettuce, with KHH13 showing superior efficacy. The study also found KHH13’s treatment enhanced the growth of various vegetables, including tomato, cucumber, and red lettuce. In terms of disease control, KHH13 significantly reduced Fusarium wilt in cucumbers, as evidenced by the reduction in disease index from 74.33% to 41.67% after KHH13 treatment. The treatment group displayed better plant growth, including plant height and fresh weight, compared to the control group in the greenhouse experiment. Furthermore, oral and pulmonary acute toxicity analysis in rats showed no adverse effects on rat weight or mortality, indicating KHH13’s safety for mammalian use. These findings suggest B. velezensis KHH13 as a safe, effective, and sustainable biological agent for enhancing vegetable growth and controlling soil-borne diseases, with potential applications in sustainable agriculture.