A two-dimensional (2D) Si film can form between a graphene overlayer and a Ru(0001) substrate through an intercalation process. At the graphene/2D-Si/Ru(0001) surface, the topmost graphene layer is decoupled from the Ru substrate and becomes quasi-freestanding. The interfacial Si layers show high stability due to the protection from the graphene cover. Surface science measurements indicate that the surface Si atoms can penetrate through the graphene lattice, and density functional theory calculations suggest a Si-C exchange mechanism facilitates the penetration of Si at mild temperatures. The new mechanism may be involved for other elements on graphene, if they can bond strongly with carbon. This finding opens a new route to form 2D interfa...