By using an alternative wet-etch procedure, we have obtained high-quality atomically flat TiO2 terminated surfaces of SrTiO3 single crystals with the morphology equivalent to that of the conventional wet-etch methods. By applying a combined power of photoluminescence (PL) spectroscopy, reflection high-energy electron diffraction, atomic force microscopy imaging, and soft x-ray absorption (XAS), we were able to identify and monitor the complex evolution of oxygen defect states and Ti valency at the surface and near-surface layers. Our experiments revealed a high level of local defects resulting in the presence of the Ti3+ states at the surface. We have developed a method to control the defect states capable of a marked reduction of the defect concentration. We have demonstrated that the PL and XAS are able to distinguish the surface-related Ti3+ states from oxygen vacancies trapping charge transfer vibronic excitons that define the PL intensity. The experimental findings will have important implications for the growth of high-quality ultrathin complex oxide heterostructures.