Intercalation is the process of inserting chemical species into the heterointerfaces of two-dimensional (2D) layered materials. While much research has focused on the intercalation of metals and small gas molecules into graphene, the intercalation of larger molecules through the basal plane of graphene remains challenging. In this work, we present a new mechanism for intercalating large molecules through monolayer graphene to form confined oxide materials at the graphene-substrate heterointerface. We investigate the intercalation of phosphorus pentoxide (P2O5) molecules directly from the vapor phase and confirm the formation of confined P2O5 at the graphene-substrate heterointerface using various techniques. Density functional theory (DFT) corroborates the experimental results and reveals the intercalation mechanism, whereby P2O5 dissociates into small fragments catalyzed by defects in the graphene that then permeates through lattice defects and reacts at the heterointerface to form P2O5. This process can also be used to form new confined metal phosphates (e.g., 2D InPO4). While the focus of this study is on P2O5 intercalation, the possibility of intercalation from predissociated molecules catalyzed by defects in graphene may exist for other types of molecules as well. This in-depth study advances our understanding of intercalation routes of large molecules via the basal plane of graphene as well as heterointerface chemical reactions leading to the formation of distinctive confined complex oxide compounds.