Botrytis cinerea is a destructive phytopathogenic ascomycete causing severe pre- and postharvest yield losses in tomato-growing areas worldwide. Due to fungicide resistance development in B. cinerea strains, its chemical control has become a serious challenge for tomato growers. In the present investigation, 47 fungal isolates were obtained and screened for their biocontrol potency against B. cinerea, and 12 isolates showed significant biocontrol efficacy. In 12 fungal bioagents, Trichoderma harzianum isolate Tr‑3, identified by internal transcribed spacer (ITS) region sequence analysis, significantly suppressed the in vitro mycelial growth of B. cinerea. Furthermore, different concentrations (10, 25, 50, and 100 ppm) of zinc nanoparticles (ZnO-NPs) demonstrated remarkable suppression of in vitro mycelial growth. At higher concentrations (100 ppm) of ZnO-NPs, 88% mycelial growth inhibition of the pathogen was recorded. Moreover, foliar applications of T. harzianum suspension and ZnO-NPs in the greenhouse provided a promising control of B. cinerea infection in tomato plants, and a significant reduction in disease severity (68.5 and 83.4%, respectively) was recorded. While the foliar applications attenuate disease intensity, a significant increase in plant biomass was also recorded, which demonstrated the plant growth-promoting potential of indigenous T. harzianum and ZnO-NPs. Additionally, the antioxidant and phytochemical analysis of treated tomato leaves demonstrated higher levels of catalase (CAT) and peroxidase (PO) activity in ZnO-NP-treated plants followed by T. harzianum-treated plants. Thus, these results suggested that ZnO-NPs and indigenous T. harzianum as biocontrol could suppress B. cinerea infection in the greenhouse, either directly or indirectly as resistance inducers. Therefore, ZnO-NPs and T. harzianum may be applied as an alternative to fungicides to alleviate gray mold disease in tomato caused by the resistance problems in B. cinerea.