Nanoparticle clusters with molecular-like configurations are an emerging class of colloidal materials. Particles decorated with attractive surface patches acting as analogs of functional groups are used to assemble colloidal molecules (CMs); however, high-yield generation of patchy nanoparticles remains a challenge. We show that for nanoparticles capped with complementary reactive polymers, a stoichiometric reaction leads to reorganization of the uniform ligand shell and self-limiting nanoparticle bonding, whereas electrostatic repulsion between colloidal bonds governs CM symmetry. This mechanism enables high-yield CM generation and their programmable organization in hierarchical nanostructures. Our work bridges the gap between covalent bonding taking place at an atomic level and colloidal bonding occurring at the length scale two orders of magnitude larger and broadens the methods for nanomaterial fabrication.