Metal semiconductor alloy contacts are provided on each of a source region and a drain region which are present in a semiconductor substrate. A transition metal is then deposited on each of the metal semiconductor alloy contacts, and during the deposition of the transition metal, the deposited transition metal reacts preferably, but not necessarily always, in-situ with a portion of each the metal semiconductor alloy contacts forming a transition metal-metal semiconductor alloy liner atop each metal semiconductor alloy contact. Each transition metal-metal semiconductor alloy liner that is provided has outer edges that are vertically coincident with outer edges of each metal semiconductor alloy contact. The transition metal-metal semiconductor alloy liner is more etch resistant as compared to the underlying metal semiconductor alloy. As such, the transition metal-metal semiconductor alloy liner can serve as an effective etch stop layer during any subsequently performed etch process.