We demonstrate that electron irradiation of colloidal CdS nanorods carrying Au domains causes their evolution into AuS/Cd core/shell nanoparticles as a result of a concurrent chemical and morphological transformation. The shrinkage of the CdS nanorods and the growth of the Cd shell around the Au tips are imaged in real time, while the displacement of S atoms from the CdS nanorod to the Au domains is evidenced by high-sensitivity energy-dispersive X-ray (EDX) spectroscopy. The various nanodomains display different susceptibility to the irradiation, which results in nanoconfigurations that are very different from those obtained after thermal annealing. Such physical manipulations of colloidal nanocrystals can be exploited as a tool to access novel nanocrystal heterostructures.