Distance measurements via the dipolar interaction are fundamental to the application of nuclear magnetic resonance (NMR) to molecular structure determination, but they only provide information on the absolute distance $r$ and polar angle $theta$ between spins. In this Letter, we present a protocol to also retrieve the azimuth angle $phi$. Our method relies on measuring the nuclear precession phase after application of a control pulse with a calibrated external radio-frequency coil. We experimentally demonstrate three-dimensional positioning of individual carbon-13 nuclear spins in a diamond host crystal relative to the central electronic spin of a single nitrogen-vacancy center. The ability to pinpoint three-dimensional nuclear locations is central for realizing a nanoscale NMR technique that can image the structure of single molecules with atomic resolution.