Derivatives of Carya illinoinensis (pecan) are used as dietary supplements and their leaf and nuts-in-shuck extracts are used in the treatment of various pathologies due to their significant composition in phenolic compounds that act as natural antifungal and anticancer agents. This study aimed to evaluate the antifungal activity of acetone extracts (AEs) from leaves (L) and nuts-in-shucks (S) of cultivars (cv.) Wichita (Wic) and Ukulinga (Uku) of South African C. illinoinensis against A. alternata pathogen. The AEs of Wic-L and Uku-L showed higher antifungal efficacy against all tested A. alternata isolates, with inhibition zones ranging from 11 to 39 mm. Acetone crude extracts of cv. Wichita and cv. Ukulinga showed efficacy against the isolates and were significantly different (p < 0.001). Scanning electron microscopy (SEM) showed major morphological damages on the conidia from assayed cultures, which resulted in inhibition. We further evaluated the in vitro cytotoxic effects of Carya illinoinensis on human embryonic kidney 293 (HEK-293T) cell lines with methanolic extracts (MEs). HEK-293T cell lines (10 × 103 cells/well) were treated with each sample of the extracts at various concentration (1.56, 6.25, 12.5, 25, 50, and 100 µg/mL) and cell viability was quantitated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay after 48 h. The HEK-293 cell viabilities when exposed to MEs of Wic-L, Wic-S, and Uku-L were 88.2%, 75.2%, and 86.3% respectively, confirming non-toxic properties in accordance with International Organisation for Standardization (ISO) norms. However, the viability of cell culture after the treatment with MEs of Uku-S was 37% and was as toxic. We further used High-performance liquid chromatography (HPLC) to investigate individual phenolic constituents and total phenolic content in the leaves and shucks of both cultivars. Twelve individual phenols were detected through HPLC analysis in the respective extracts. The total phenolic content was higher in the extracts of Wic-L (102.19 mg GAE/g) and Uku-L (110.13 mg GAE/g) relative to the Wic-S (62.03 mg GAE/g) and Uku-S (85.07 mg GAE/g) extracts. Finally, these findings highlighted the possibility of pecan leaf extracts as a potential natural bioactive antifungal agent against black spot disease on pecans in South Africa.