In this study, we investigated the effects of infant fecal fermentation-derived metabolites of digested osteopontin (OPN) and 2′-fucosyllactose (2′-FL), either individually or in combination, on intestinal barrier function using a Caco-2/HT-29 coculture cell model. Our results suggested that the OPN/2′-FL (1:36−1:3) cofermentation metabolites improved epithelial barrier integrity by supporting the mRNA and protein expression of occludin, claudin-1, claudin-2, ZO-1, and ZO-2. All of the OPN/2′-FL treatments decreased the production of IL-1β, IL-6, and TNF-α, while the OPN/2′-FL ratio increased IL-10 production by inhibiting activation of the MyD88/IκB-α/NF-κB signaling pathway. OPN/2′-FL cofermentation altered the metabolic pathways, and the protective effect of fermentation metabolites on intestinal barrier function was related to differential metabolite expression such as short-chain fatty acids, deoxycholic acid, and 4-aminobutyric acid. Our findings provide in vitro evidence to support the application of the OPN/2′-FL combination in infant formula for the advancement of formulation functionality, including intestinal barrier function.