Crop diseases caused by Fusarium pathogens, among other microorganisms, threaten crop production in both commercial and smallholder farming. There are increasing concerns about the use of conventional synthetic fungicides due to fungal resistance and the associated negative effects of these chemicals on human health, livestock and the environment. This leads to the search for alternative fungicides from nature, especially from plants. The objectives of this study were to characterize isolated compounds from Combretum erythrophyllum (Burch.) Sond. and Withania somnifera (L.) Dunal leaf extracts, evaluate their antifungal activity against Fusarium pathogens, their phytotoxicity on maize seed germination and their cytotoxicity effect on Raw 264.7 macrophage cells. The investigation led to the isolation of antifungal compounds characterized as 5-hydroxy-7,4′-dimethoxyflavone, maslinic acid (21-hydroxy-3-oxo-olean-12-en-28-oic acid) and withaferin A (4β,27-dihydroxy-1-oxo-5β,6β-epoxywitha-2-24-dienolide). The structural elucidation of the isolated compounds was established using nuclear magnetic resonance (NMR) spectroscopy, mass spectroscopy (MS) and, in comparison, with the available published data. These compounds showed good antifungal activity with minimum inhibitory concentrations (MIC) less than 1.0 mg/mL against one or more of the tested Fusarium pathogens (F. oxysporum, F. verticilloides, F. subglutinans, F. proliferatum, F. solani, F. graminearum, F. chlamydosporum and F. semitectum). The findings from this study indicate that medicinal plants are a good source of natural antifungals. Furthermore, the isolated antifungal compounds did not show any phytotoxic effects on maize seed germination. The toxicity of the compounds A (5-hydroxy-7,4′-dimethoxyflavone) and AI (4β,27-dihydroxy-1-oxo-5β,6β-epoxywitha-2-24-dienolide) was dose-dependent, while compound B (21-hydroxy-3-oxo-olean-12-en-28-oic acid) showed no toxicity effect against Raw 264.7 macrophage cells.