Parasitic two-level tunnelling systems originating from structural material defects affect the functionality of various microfabricated devices by acting as a source of noise. In particular, superconducting quantum bits may be sensitive to even single defects when these reside in the tunnel barrier of the qubits Josephson junctions, and this can be exploited to observe and manipulate the quantum states of individual tunnelling systems. Here, we detect and fully characterize a system of two strongly interacting defects using a novel technique for high-resolution spectroscopy. Mutual defect coupling has been conjectured to explain various anomalies of glasses, and was recently suggested as the origin of low-frequency noise in superconducting devices. Our study provides conclusive evidence of defect interactions with full access to the individual constituents, demonstrating the potential of superconducting qubits for studying material defects. All our observations are consistent with the assumption that defects are generated by atomic tunnelling.