Aspergillus ochraceus (A. ochraceus) contamination and ochratoxin A (OTA) production in cereals time to time induced significant public health concerns. In this study, the inhibitory effects and mechanisms of five lactic acid bacteria (LAB) strains on A. ochraceus were investigated by monitoring mycelium growth, spore germination, morphologic alterations, DNA damage, OTA concentration, and OTA-production-related genes expression. Among the five LAB strains examined, Lactobacillus amylolyticus L6 demonstrated the strongest antifungal effectiveness. Significant downregulation of OTA biotransformation and secondary metabolism-related genes was observed, leading to decreased OTA production in the tested fungistat. Moreover, partial least squares discriminant analysis identified hydroxy-3-methoxycinnamic acid and 3,7-dimethyl-2,6-octadienol as the metabolites most likely responsible for L6's inhibition against A. ochraceus. This was further verified by quantifying these two metabolites in L6-fermented supernatant, with concentrations of 14.304 ± 0.016 and 0.184 ± 0.009 mg/mL, respectively, close to their minimal inhibitory concentrations (MIC) of 20.00 and 0.20 mg/mL. ITS genomic analysis showed that L6 significantly reduced the abundance of Aspergillus in breads made from all-purpose flour (APF) and whole flour (WF), suggesting promising applications in the food industry. These findings provide a strong potential for utilizing L6 to control fungal contamination in cereals.