A method for forming a metal-semiconductor alloy layer uses particular thermal annealing conditions to provide a stress free metal-semiconductor alloy layer through interdiffusion of a buried semiconductor material layer and a metal-semiconductor alloy forming metal layer that contacts the buried semiconductor material layer within an aperture through a capping layer beneath which is buried the semiconductor material layer. A resulting semiconductor structure includes the metal-semiconductor alloy layer that further includes an interconnect portion beneath the capping layer and a contiguous via portion that penetrates at least partially through the capping layer. Such a metal-semiconductor alloy layer may be located interposed between a substrate and a semiconductor device having an active doped region.