At least one doped silicon region is formed in a silicon layer of a semiconductor substrate, and a silicon oxide layer is formed over the silicon layer. A germanium-containing material portion is formed in the semiconductor substrate to provide a p-n junction or a p-i-n junction including the germanium-containing material portion and one of the at least one doped silicon region. A capping material layer that is free of germanium is formed over the germanium-containing material portion. A first dielectric material layer is formed over the silicon oxide layer and the capping material layer. The first dielectric material layer includes a mesa region that is raised from the germanium-containing material portion by a thickness of the capping material layer. The capping material layer may be a silicon capping layer, or may be subsequently removed to form a cavity. Dark current is reduced for the germanium-containing material portion.