Aflatoxins are a large group of highly toxic, mutagenic, and carcinogenic mycotoxins produced by specific species of fungi. Potential contamination of food commodities by these compounds causes extensive damage that lead to great economic losses. This study explored the potential use of antifungal compounds, produced by Lactobacillus brevis and Lactobacillus paracasei, for growth inhibition and subsequent aflatoxin B1 production from select strains of Aspergillus flavus and Aspergillus parasiticus. Lactobacilli strains were isolated from traditional Egyptian dairy products, whereas fungal strains were isolated from infected cereal seeds. There were noticeable decreases in mycelium biomass and aflatoxin production as well. L. brevis exhibited the highest reduction of aflatoxin B1 production by A. flavus and A. parasiticus, 96.31 and 90.43%, respectively. The concentrations of amino acids of the antifungal compound produced by L. brevis were significantly higher than that produced by L. paracasei. Asparagine, glutamine, glycine, alanine, and leucine were the most concentrated amino acids for both strains. The antifungal compounds produced by L. brevis and L. paracasei were active in a wide range of pH, heat stable and inactivated by proteolytic enzymes (protease K and trypsin A). The expression of Omt-A gene that involved in the later step of aflatoxin production was evaluated by real-time PCR. There was a vigorous reduction at transcriptional level of Omt-A gene observed in A. flavus that is treated by L. brevis and L. paracasei (80 and 70%, respectively). However, the reduction of Omt-A gene observed in A. parasiticus that is treated by L. brevis and L. paracasei was 64.5 and 52%, respectively. Treating maize seeds with antifungal compounds exhibited great efficiency in controlling fungal infection and increasing seed germination. The results confirmed that lactic acid bacteria are a promising strategy to control food contamination of fermented food and dairy products.