We provide a direct experimental proof and the related modeling of the role played by Si overgrowth in promoting the lateral ordering of Ge islands grown by chemical vapor deposition on Si(001). The deposition of silicon induces a shape transformation, from domes to truncated pyramids with a larger base, generating an array of closely spaced interacting islands. By modeling, we show that the resulting gradient in the chemical potential across the island should be the driving force for a selective flow of both Ge and Si atoms at the surface and, in turn, to a real motion of the dots, favoring the lateral order.