Nucleotides—the structural units of nucleic acids—function not merely as metabolites but as fully-fledged pharmacologically active substances with well-characterized receptor and molecular mechanisms of action. The fermented milk bacterial-yeast beverage with high nucleic acid content combines the pharmacological activity of nucleotides with probiotic and prebiotic effects, positioning it as a unique natural immunomodulator fundamentally distinct from synthetic immunotropic agents. Objective: To systematically synthesize scientific evidence regarding the pharmacological status of dietary nucleotides—including mechanisms of action, classification, pharmacodynamics, and position within the immunotropic agent framework—and to consolidate clinical data on the efficacy of the bacterial-yeast beverage in secondary immunodeficiency states and related pathological conditions. Methods: Narrative literature review (PubMed/MEDLINE, Scopus, WoS, 2000–2025) combined with the author's own clinical and laboratory investigations (1993–2016). Results: Nucleotides from the bacterial-yeast beverage exert pharmacological activity through: (1) TLR9 agonism (CpG-DNA → MyD88 → NF-κB → Type I IFN, IL-12); (2) salvage pathway utilization—supporting lymphocyte and enterocyte proliferation; (3) purinergic signaling (adenosine → A₂A receptors → cAMP → immunoregulation); and (4) Nod-like receptor (NLR) activation. Clinically: post-vaccination immunity enhancement by 15–22%, CD4⁺/CD8⁺ ratio and phagocytic index correction, and sIgA normalization. Unlike pharmaceutical immunotropic agents, the beverage's nucleotides act synphysiologically—through the same receptor systems activated during natural immune responses. Conclusion: The fermented milk bacterial-yeast beverage represents a pharmacologically substantiated, multi-target natural immunomodulator. Its advantages over synthetic immunotropic agents include: pleiotropic pharmacodynamics, physiological route of administration, absence of receptor saturation, probiotic and microbiome-normalizing effects, and population-level accessibility. Its inclusion in clinical nutrition standards for secondary immunodeficiency states is warranted.