Products enriched with probiotic microorganisms have proven to possess immunomodulatory, antioxidant, hypo-cholesterolemic, hypotensive, and antimicrobial properties. Biologically active substances, which are by-products of microbial fermentation, have potential applications in various industries. Cell-free supernatants, depending on the microorganisms used and production conditions, can exhibit antimicrobial, antioxidant, bifidogenic, and other biological activities. This paper presents a study on the biological activity of a probiotic fermented milk product, supplemented with 0.01% lyophilized cell-free supernatant from Lactobacillus helveticus. The fermented milk product was developed based on a composition of Lacticaseibacillus rhamnosus F, Lactococcus cremoris CR201, and Propionibacterium shermanii E2. The research evaluated antimicrobial activity, Bifidobacteria growth stimulation, and the content of organic acids, amino acids, and B vitamins. It was found that adding lyophilized cell-free supernatant to the fermented milk product enhanced its biological activity. In particular, the experimental samples showed a threefold increase in vitamin B6 content compared to the control, reaching 22.412 μg/100 g. Additionally, the amino acid content in the experimental samples exhibited a significant increase of more than 100% in the essential amino acid tryptophan compared to the control. Notably, antimicrobial activity increased against several opportunistic strains. The experimental samples also showed a significant increase in lactic and formic acids, which may enhance the product’s inhibitory properties against pathogens. An increase in antioxidant activity was observed, potentially due to the higher content of tryptophan and vitamin B6. The positive effect of adding cell-free supernatant on the growth of Bifidobacteria was also demonstrated. Thus, the findings suggest that this cell-free supernatant can be recommended as an additive in the production of fermented milk products, food additives, dietary supplements, and animal feed.