Pathogenicity tests of Fusarium oxysporum Schltdl. isolates on tomato (Solanum lycopersicum L.) demonstrated a significant capacity to induce seed rot and seedling damping-off under greenhouse conditions. The most virulent isolate, confirmed via polymerase chain reaction (PCR), was selected for further study. Inoculation with Trichoderma harzianum and mycorrhizal fungi substantially enhanced the total phenolic content and peroxidase (POX) enzyme activity in F. oxysporum-infected plants. Furthermore, high-performance liquid chromatography (HPLC) analysis revealed that these biological control agents significantly boosted the biosynthesis of key secondary metabolites, specifically the glycoalkaloids (GAs) α-tomatine, tomatidine and solanine. The interaction between F. oxysporum and T. harzianum resulted in the highest accumulation of these defense-related compounds compared to plants infected with the pathogen alone. These findings suggest that T. harzianum and mycorrhizal fungi activate the plant’s systemic resistance by modulating physiological and biochemical defense mechanisms against Fusarium wilt.