Enhanced yield of tomato has ever been an important issue due to its nutritional value and various dietary consumption forms. But, efficient yield increase can never be achieved without using environmentally safe means e.g. innate resistance. In present study, tomato innate antifungal resistance has been boosted up using Penicillium oxalicum, and then various aspects of resistance modulation have been explored in details. Two tomato varieties of differential antifungal resistance (Dinaar and Red Tara) were treated with six P. oxalicum strains which screened the best inducer strain (Pn 5); which remarkably controlled disease incidence (DI) of Alternaria alternata. Inducer was not only responsible for almost two times production of phenolics, alkaloids and terpenoids in Red Tara, but it also non-significantly triggered same biochemicals in Dinaar. Hemicellulose showed only 40 % increase in variety of least antifungal resistance. During quantification assays of peroxidase (POD), phenyl ammonia lyase and polyphenol oxidase, more or less the same doubling trend was recorded in susceptible variety, while only POD had significant enhancement in resistant variety under the influence of fungal inducer. It was also recorded that inducer not only modulated quantity of enzyme (glucanase), but its isozyme package was also altered. Colorimetric quantifications of lignin, cellulose and pectins proved that biotic inducer strengthened the physical structure of plant cells by increasing these contents from 30 to 120 %. The above investigation collectively comes with the recommendation of an efficient and environmentally safe inducer (P. oxalicum); which, can be used to control fungal pathogens.