Bacillus subtilis E20-fermented soybean meal (FSBM) was found to produce antimicrobial peptides (AMPs) with great antimicrobial activity against Vibrio alginolyticus (VA) and V. parahaemolyticus (VP). Three AMPs were purified with a 5 kDa ultrafiltration, Sephadex G-15 column and reverse-phase high-performance liquid chromatography (RP-HPLC). The FSB-AMP, HTSKALLDMLKRLGK, identified by an RP-nano-ultrapure liquid chromatography (UPLC) electrospray ionization (ESI)-tandem mass spectroscopic (MS/MS) analysis exhibited the highest bactericidal activity against VA and VP compared to the others. The antimicrobial activity assessment indicated that FSB-AMP inhibited the growth of VA and VP with minimal inhibitory concentrations of 72.5 and 72.5 μM. Alterations in the morphology of VA were observed by scanning electronic microscopy, and membrane disruption of VA and VP was confirmed by fluorescent microscopy with propidium iodide staining. The FSB-AMP was then incorporated into the diet of white shrimp, Litopenaeus vannamei, and a protective effect in shrimp against VP infection was recorded as well as for shrimp fed a diet containing 15% fish meal replaced by B. subtilis E20-FSBM. Results demonstrated that B. subtilis E20-FSBM could be a biofunctional ingredient to prevent vibriosis in shrimp aquaculture.