In vitro and in vivo assays evaluated commercial Bacillus-based probiotics (feed-applied PRO-2 and water-applied PRO-W) and a potassium peroxymonosulfate disinfectant (PUR) against Vibrio parahaemolyticus (VPAHPND) and Vibrio harveyi in Pacific white shrimp (Litopenaeus vannamei). In vitro co-cultures demonstrated that probiotic Bacillus strains suppressed pathogen growth, while PUR showed strong bactericidal activity with a minimum bactericidal concentration (MBC) of 5000 ppm. In feeding trials, administering PRO-2 at 1 or 5 g/kg feed for 4 weeks significantly increased shrimp survival following VPAHPND challenge (76.67% and 90.00%, respectively, vs. 6.67% in control). For V. harveyi challenge, dietary PRO-2 at 1 g/kg yielded 96.67% survival compared to 70.00% in control shrimp. Water treatment with PRO-W at 2 × 10^6 g/ha for 7 days also enhanced survival up to 40.0% against VPAHPND and 33.3% against V. harveyi. Tolerable PUR concentrations in rearing water (0.5–10 ppm) did not confer disease protection during bacterial challenge, indicating that PUR is best suited for pond preparation and biosecurity sanitation at high concentrations. Overall, regular probiotic administration effectively manages pathogenic Vibrio in shrimp culture.