The exact location of a single dopant atom in a nanostructure can influence or fully determine the functionality of highly scaled transistors or spin-based devices. We demonstrate here a noninvasive spatial metrology technique, based on the microscopic modeling of three electrical measurements on a single-atom (phosphorus in silicon) spin qubit device: hyperfine coupling, ground state energy, and capacitive coupling to nearby gates. This technique allows us to locate the qubit atom with a precision of ±2.5 nm in two directions and ±15 nm in the third direction, which represents a 1500-fold improvement with respect to the prefabrication statistics obtainable from the ion implantation parameters.