The tomato crop is susceptible to various types of stress, both biotic and abiotic, which affect the morphology, physiology, biochemistry, and genetic regulation of plants. Among the biotic factors, is the phytopathogenFusarium oxysporumf. sp.lycopersici(Fol), which can cause losses of up to 100%. Graphene–Cu nanocomposites have emerged as a potential alternative for pathogen control, thanks to their antimicrobial activity and their ability to induce the activation of the antioxidant defense system in plants. In the present study, the effect of the Graphene–Cu nanocomposites and the functionalization of graphene in the tomato crop inoculated with Fol was evaluated, analyzing their impacts on the antioxidant defense system, the foliar water potential (Ψh), and the efficiency of photosystem II (PSII). The results demonstrated multiple positive effects; in particular, the Graphene–Cu nanocomposite managed to delay the incidence of the “vascular wilt” disease and reduce the severity by 29.0%. This translated into an increase in the content of photosynthetic pigments and an increase in fruit production compared with Fol. In addition, the antioxidant system of the plants was improved, increasing the content of glutathione, flavonoids, and anthocyanins, and the activity of the GPX, PAL, and CAT enzymes. Regarding the impact on the water potential and the efficiency of the PSII, the plants inoculated with Fol and treated with the Graphene–Cu nanocomposite responded better to biotic stress compared with Fol, reducing water potential by up to 31.7% and Fv/Fm levels by 32.0%.