This study aimed to identify a probiotic bacterium with antagonistic activity against the foodborne pathogen Staphylococcus aureus (S. aureus) and investigate the mechanism of its antibacterial components. Growth kinetics were analyzed to assess bacterial proliferation. Acid and bile salt tolerance are vital indicators for evaluating probiotic survival in the gastrointestinal tract. The results indicated that Companilactobacillus farciminis (C. farciminis) YLR-1 not only had high tolerance to salt conditions (0.03%, 0.3%, and 0.5%) but also has a high survival rate at pH 3–4. The bacteriocin-like inhibitory substance (BLIS) isolated from C. farciminis YLR-1 was dialyzed using a membrane with a molecular weight cut-off (MWCO) of 500 Da, followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The results indicate that the BLIS produced by C. farciminis YLR-1 is a small-molecule peptide. BLIS displayed pH tolerance within acidic and neutral environments (4–8) and exhibited thermostability. When treated with proteinase K, the antibacterial action of BLIS was found to be inactivated. Membrane disruption mechanisms were examined using fluorescence imaging and scanning electron microscopy (SEM). SEM and fluorescence imaging revealed that BLIS-induced membrane damage in S. aureus ATCC 25923 causes cytoplasmic leakage and cell death.