Powdery mildew is a pervasive fungal disease causing significant economic losses globally. Continuous use of synthetic fungicides has led to environmental concerns and resistant fungal strains. This study explores marine-derived cephalostatins from the South African Natural Compounds Database as novel fungicidal agents for managing powdery mildew. Using molecular docking techniques, we investigated the interaction between selected cephalostatins and critical proteins involved in powdery mildew pathogenesis. Compounds were selected based on drug-likeness and bioactivity, adhering to Lipinski’s Rule of Five. Molecular interactions, binding affinities, and stability were analysed using AutoDock Vina, PyMOL, and Discovery Studio. Cephalostatin 17 exhibited the highest binding affinity (−10.4 kcal/mol), indicating strong potential for inhibiting fungal growth through significant hydrogen bonding and hydrophobic interactions. The study’s primary limitation is the reliance on computational predictions, necessitating experimental validation. Cephalostatin 17 stands out as a promising candidate for sustainable agricultural practices.