A structural phase transition has been discovered in the synthetic tetrahedrite Cu12Sb4S13 at approximately 88 K. Upon cooling, the material transforms from its known cubic symmetry to a tetragonal unit cell that is characterized by an in-plane ordering that leads to a doubling of the unit cell volume. Specific heat capacity measurements demonstrate a hysteresis of more than two degrees in the associated anomaly. Similar hysteresis was observed in powder x-ray diffraction measurements that also indicate a coexistence of the two phases, and together these results suggest a first order transition. This structural transition coincides with a recently-reported metal-insulator transition, and the structural instability is related to the very low thermal conductivity κ in these materials. Inelastic neutron scattering was used to measure the phonon density of states in Cu12Sb4S13 and Cu10Zn2Sb4S13, both of which possess a localized, low-energy phonon mode associated with strongly anharmonic copper displacements that suppress κ. In Cu12Sb4S13, signatures of the phase transition are observed in the temperature dependence of the localized mode, which disappears at the structural transition. In contrast, in the cubic Zn-doped material the mode is at slightly higher-energy but observable for all temperatures, though it softens upon cooling.