Punica granatum L. (pomegranate) is a rich source of natural antioxidants, particularly polyphenols, which exhibit anti-inflammatory, anti-tumorigenic, and antimicrobial properties. This study aimed to evaluate the effect of pomegranate peel aqueous extracts on rabbit incisional wounds compared to a chemical pharmaceutical product used for the same purpose. In this study, a 7.5% P. granatum aqueous peel extract was formulated as a topical ointment and assessed for its wound-healing potential in rabbits in vivo. Three groups of rabbits (n = 5 per group) received incisional wounds and were treated with either pomegranate peel ointment, Fucidin® antibiotic, or left untreated as a control. The antioxidant properties of pomegranate seeds, outer peels, and inner peels were analyzed using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay, alongside phenolic composition and flavonoid content screening. The results of this study indicate that aqueous peel extracts exhibit higher radical scavenging activity than seed extracts. Furthermore, the topical pomegranate peel ointment demonstrated wound-healing efficiency comparable to the commercial antibiotic, facilitating complete healing within eight days without complications. These findings suggest that a natural, aqueous-based pomegranate peel ointment could serve as a potential alternative to synthetic antibiotics for treating incisional wounds.