The dynamic properties of assembled structures are governed by the substructure dynamics as well as the dynamics of the joints that are part of the assembly. It can be challenging to describe the physical interactions within the joints analytically, as slight modifications, such as static preload, temperature, etc. can lead to significant changes in the assembly’s dynamic properties. Therefore, characterizing the dynamic properties of joints typically involves experimental testing and subsequent model updating. In this paper, a machine-learning-based approach to joint identification is proposed that utilizes a physics-based computational model of the joint. The idea is to combine the computational model of the joint with dynamic substructuring techniques to train the machine-learning model. The flexibility of dynamic substructuring permits the enforcement of compatibility and equilibrium conditions between the component models from the experimental and numerical domains, facilitating the development of machine-learning models that can predict the dynamic properties of joints. The proposed approach provides an accurate data-driven method for joint identification in real structures, while reducing the number of measurements needed for the identification. The approach permits the identification of a full 12-DoF joint, enabling the coupling of 3D dynamic models of substructures. Compared to the standard decoupling approach, no spurious peaks are present in the reconstructed assembly response. The proposed approach is validated numerically and experimentally by reconstructing the assembly response and comparing the results with known assembly dynamics.