Tomato pomace (TP), an antioxidant-rich byproduct, may be suitable for noble applications. The regulation of ROS generation and the anti-inflammatory response can help to prevent ulceration. The purpose of this study was to examine TP for antioxidants, in silico anti-inflammatory properties, and its potential to protect against ulceration and erosion triggered by indomethacin. Tomato pomace extract (TPE) was encapsulated either alone or with probiotics to maximize its potential effect. These microcapsules were investigated in indomethacin-treated rats. TPE demonstrated antioxidant activity as well as high levels of carotenoids (15 mg/g extract) and polyphenols. Because of their binding affinity as well as hydrophobic and hydrogen bond interactions with the active sites of TNF-α and IL-1β inflammatory cytokines, ellagic acid and rutin may be implicated in the anti-inflammatory effect of TPE, according to the docking study. TPE microcapsules, either alone or in combination with probiotics, demonstrated a protective effect against enterocolitis by reducing oxidative stress and inflammation, as evidenced by the decrease in stomach and intestinal MDA, NO, IL-1β, IL-6, and TNF-α levels and the increase in CAT, SOD, and GSH activities. The produced microcapsules are suggested to be promising candidates for protection against gastric ulcers and erosion.