High integrity shallow source/drain junctions are formed employing cobalt silicide contacts. A layer of cobalt and a cap layer of titanium or titanium nitride are deposited on a substrate above intended source/drain regions, followed by silicidation. Embodiments include low-temperature rapid thermal annealing to form a high-resistivity phase cobalt silicide, removing the cap layer, depositing a doped film on the first phase cobalt silicide, and heating, as by high-temperature rapid thermal annealing, to form a low-resistance cobalt silicide during which impurities from the doped film diffuse through the cobalt silicide into the substrate to form source/drain regions having junctions extending into the substrate a constant depth below the cobalt silicide/silicon substrate interface. In another embodiment, impurities are diffused from the doped film to form source/drain regions and self-aligned junctions following formation of the low-resistance phase cobalt silicide. The formation of source/drain junctions self-aligned to the cobalt silicide/silicon substrate interface prevents junction leakage while allowing the formation of cobalt silicide contacts at optimum thickness to avoid parasitic series resistances, thereby facilitating reliable device scaling.