In conventional agriculture, chemical fungicides are basic mean to manage plant diseases. At commercial level application of fungicides is cumbersome and some have been proved carcinogenic. Experiments were performed in vivo with commercially available fungicides i.e. benedict (iprobenfos), treaty (tebuconazole), hiten (fentin hydroxide) and wisdom (fosetyl-aluminium) to investigate polygonal interaction of host-pathogen-fungicides in term of growth, protein and gene expression in Solanum lycopersicum. Fungicides phytotoxicity resulted in stunted growth of plant along with chlorosis and necrotic burning on leaves that resulted in reduction of growth and biomass of the infected tomato seedling. Protein profiling by SDS-PAGE exposed some new bands, and peroxidase and chitinase genes expressed appropriately after pathogen infection and fungicides application. These results suggested that fungicides may induce/activate defense related proteins in tomato against invasion of F. oxysporum f. sp. lycopersici, however deleterious phytotoxicity of fungicides hinder their proper functioning in plant.