Each of a first substrate and a second substrate includes a surface having a diffusion resistant dielectric material such as silicon nitride. Recessed regions are formed in the diffusion resistant dielectric material and filled with a bondable dielectric material. The patterns of the metal pads and bondable dielectric material portions in the first and second substrates can have a mirror symmetry. The first and second substrates are brought into physical contact and bonded employing contacts between metal pads and contacts between the bondable dielectric material portions. Through-substrate-via (TSV) structures are formed through bonded dielectric material portions. The interface between each pair of bonded dielectric material portions located around a TSV structure is encapsulated by two diffusion resistant dielectric material layers so that diffusion of metal at a bonding interface is contained within each pair of bonded dielectric material portions.