The formation of regularly spaced metal nanostructures in selectively placed insulating nanowires is an important step toward realization of a wide range of nanoscale electronic and optoelectronic devices. Here we report templated synthesis of Au nanospheres embedded in silica nanowires, with nanospheres consistently spaced with a period equal to three times their diameter. Under appropriate conditions, nanowires form exclusively on Si nanostructures because of enhanced local oxidation and reduced melting temperatures relative to templates with larger dimensions. We explain the spacing of the nanospheres with a general model based on a vapor-liquid-solid mechanism, in which an Au/Si alloy dendrite remains liquid in the nanotube until a critical Si concentration is achieved locally by silicon oxide-generated nanowire growth. Additional Si oxidation then locally reduces the surface energy of the Au-rich alloy by creating a new surface with smaller area inside of the nanotube. The isolated liquid domain subsequently evolves to become an Au nanosphere, and the process is repeated.