This paper presents a novel method for rapidly addressing the earthquake-induced damage identification task in historic masonry towers. The proposed method, termed DORI, combines operational modal analysis (OMA), FE modeling, rapid surrogate modeling (SM) and non-linear Incremental dynamic analysis (IDA). While OMA-based Structural Health Monitoring methods using statistical pattern recognition are known to allow the detection of small structural damages due to earthquakes, even far-field ones of moderate intensity, the combination of SM and IDA-based methods for damage localization and quantification is here proposed. The monumental bell tower of the Basilica of San Pietro located in Perugia, Italy, is considered for the validation of the method. While being continuously monitored since 2014, the bell tower experienced the main shocks of the 2016 Central Italy seismic sequence and the on-site vibration-based monitoring system detected changes in global dynamic behavior after the earthquakes. In the paper, experimental vibration data (continuous and seismic records), FE models and surrogate models of the structure are used for post-earthquake damage localization and quantification exploiting an ideal subdivision of the structure into meaningful macroelements. Results of linear and non-linear numerical modeling (SM and IDA, respectively) are successfully combined to this aim and the continuous exchange of information between the physical reality (monitoring data) and the virtual models (FE models and surrogate models) effectively enforces the Digital Twin paradigm. The earthquake-induced damage identified by both data-driven and model-based strategies is finally confirmed by in-situ visual inspections.