In this study, we utilized pomegranate peel and marine algae Ulva lactuca (U. lactuca) as rich and sustained sources of bioactive compounds to combat tomato-black spot disease. n-Hexane extracts from the peel of pomegranate (Punica granatum) (PPE) and the marine algal biomass U. lactuca (ULE) were used alone and in combinations to verify their impact against Alternaria alternata (A. alternata). The applied extracts exhibited severe destructive effects on both fungal growth and structure such as mycelia malformation, underdeveloped conidia, cell wall deformation, and shrinkage. Moreover, increased deformations and protrusions, and notch-like structures, were noticed in A. alternata mycelia treated with mixed extracts (PPE and ULE) compared to all other treatments. The protein and reduced sugar contents in tomato fruits were significantly increased in the infected fruits with A. alternata. The highest enzyme activities of pectinase, cellulase, catalase (CAT), and ascorbate peroxidase (APX) were recorded in infected tomatoes in comparison with the healthy ones. Molecular docking studies showed that each extract is rich with bioactive compounds that have a promising inhibition effect on A. alternata cellulases. Pomegranate and Ulva extract showed promising antifungal activity against A. alternata which revealed their feasibility and applicability as biocontrol agents in postharvest disease management and food preservation against fungal pathogens.