After forming a planarization dielectric layer in a replacement gate integration scheme, disposable gate structures are removed and a stack of a gate dielectric layer and a gate electrode layer is formed within recessed gate regions. Each gate electrode structure is then recessed below a topmost surface of the gate dielectric layer. A dielectric metal oxide portion is formed above each gate electrode by planarization. The dielectric metal oxide portions and gate spacers are employed as a self-aligning etch mask in combination with a patterned photoresist to expose and metalize semiconductor surfaces of a source region and an inner electrode in each embedded memory cell structure. The metalized semiconductor portions form metal semiconductor alloy straps that provide a conductive path between the inner electrode of a capacitor and the source of an access transistor.