We present a simulation-based classification approach for large deployed structures with localized operational excitations. The method extends the two-level Port-Reduced Reduced-Basis Component (PR-RBC) technique to provide faster solution estimation to the hyperbolic partial differential equation of time-domain elastodynamics with a moving load. Time-domain correlation function-based features are built in order to train classifiers such as Artificial Neural Networks and Support-Vector Machines and perform damage detection. The method is tested on a bridge-shaped structure with a moving vehicle (playing the role of a digital twin) in order to detect cracks’ existence. Such problem has 45 parameters and shows the merits of the two-level PR-RBC approach and of the correlation function-based features in the context of operational excitations, other nuisance parameters and added noise. The quality of the classification task is enhanced by the sufficiently large synthetic training dataset and the accuracy of the numerical solutions, reaching test classification errors below 0.1% for disjoint training set of size 7 × 103 and test set of size 3 × 103. Effects of the numerical solutions accuracy and of the sensors locations on the classification errors are also studied, showing the robustness of the proposed approach and the importance of constructing a rich and accurate representation of possible healthy and unhealthy states of interest.