Rational synthesis of coordinated spherical colloids is reported by site-selective growth of secondary hemispherical patches on primary spherical particles with quasi-defined coordination numbers and positions. We clarify the importance of mass transport phenomena on the site-specific secondary nucleation/growth in nanoparticulate colloidal systems. By comparing ultrasonic and conventional agitation during patch growth, we found that enhanced mass transfer is the key to controlled, homogeneous transport of the molecular precursors in a solvent onto the nanoparticles. With chemically defined nucleation sites, the surfaces of spherical silica particles were modified for use as a new kind of colloid with patches at desired coordination positions. Our observations represent a significant breakthrough in colloidal chemistry and self-assembly.