Grape pomace is a major by-product of winemaking and a rich source of phenolic compounds with antioxidant potential. The Carménère variety, emblematic of Chilean viticulture, remains underutilized despite its high anthocyanin and flavanol content. This study aimed to develop a cost-effective method to recover and stabilize bioactive compounds from Carménère grape pomace. Five extracts were obtained using ethanol–water mixtures (0–100%) and characterized by HPLC-DAD and antioxidant assays (DPPH, FRAP, ORAC-FL). The 80% ethanol extract (EET-80) showed the highest antioxidant capacity (FRAP: 2909.3 ± 37.6; ORAC-FL: 1864.3 ± 157.8 µmol TE/g dw) and was selected for microencapsulation via spray drying using maltodextrin. This scalable technique protects thermosensitive compounds and enhances their applicability. The optimized 1:50 extract-to-carrier ratio achieved high encapsulation efficiency (85.7 ± 0.7%). In Caco-2 cells, the microencapsulated extract (5–250 µg/mL) showed no alteration in metabolic activity and significantly reduced intracellular ROS levels (65% inhibition at 250 µg/mL). Solvent polarity selectively influenced polyphenol recovery—50% ethanol favored catechin (581.1 µg/g) and epicatechin (1788.3 µg/g), while 80% ethanol enhanced malvidin-3-O-glucoside (118.0 µg/g). These findings support the valorization of Carménère grape pomace as a sustainable source of antioxidants and highlight the role of microencapsulation in improving extract stability and functionality.