Simple perovskite crystals undergo structural phase transitions on cooling to low temperatures, which significantly change the material properties of the crystal. In this work, we rigorously characterize the temperature evolution of permittivity of a perovskite crystal as it undergoes phase transitions. In particular, we have undertaken precision measurements of a single crystal of Strontium Titanate from 294.6 to 5.6 K, by measuring the frequency of multiple microwave transverse electric (TE) and magnetic resonant modes simultaneously. The multi-mode microwave measurement technique of resonant frequency used in this work allows high precision determination of any induced anisotropy of the permittivity as the crystal undergoes structural phase transitions. Compared with previous results, we unequivocally show that the permittivity has an isotropic value of 316.3±2.2 at room temperature, consistent with its well-known cubic structure, and determine the onset of dielectric anisotropy as the crystal is cooled to lower temperatures. We show that the crystal exhibits uniaxial anisotropy in the permittivity below 105 K when the structure becomes tetragonal, and exhibits biaxial anisotropy in the permittivity below 51 K when the structure becomes orthorhombic.