The initial surface roughening during Ge epitaxy on Si(001) is shown to arise from an effective repulsion between S(A) surface steps and dimer vacancy lines (VLs). This step-VL interaction gradually inactivates a substantial fraction of adatom attachment sites at the growth front, causing a rapid increase in the rate of two-dimensional island nucleation. The mutual repulsion hinders the crossing of S(A) surface steps over VLs in the second layer, thus organizing the developing surface roughness into a periodic array of anisotropic 2D terraces. Isolated (105) facets forming at specific sites on this ordered template mediate the assembly of first 3D Ge islands.