A wafer temperature estimator calibrates contact-type temperature sensor measurements that are used by a temperature controller to control substrate temperature in a high temperature processing chamber. Wafer temperature estimator parameters provide an estimated wafer temperature from contact-type temperature sensor measurements. The estimator parameters are refined using non-contact-type temperature sensor measurements during periods when the substrate temperature is decreasing or the heaters are off. A corresponding temperature control system includes a heater, a contact-type temperature sensor in close proximity to the substrate, and an optical pyrometer placed to read temperature directly from the substrate. A wafer temperature estimator uses the estimator parameters and measurements from the contact-type sensor to determine an estimated wafer temperature. A temperature controller reads the estimated wafer temperature and makes changes to the heater power accordingly. The wafer temperature estimator has a nonlinear neural network system that is trained using inputs from the various sensors.