Superconducting circuits can coherently couple to single microscopic objects. In phase circuits, the presence of microscopic defects inside the Josephson junction was detected through qubit experiments. We now measure the case of a three-level (qutrit) system coupled to a two-level defect in the spectral domain. We then reproduce these results by simulation with no fit parameters. The ability to dynamically modify the qutrit energy levels during the excitation will allow us to probe the defect coherence and generate non-trivial entangled states for the coupled system.  The Josephson circuit is thus viewed as a coherent contact for manipulating single atomic sized defects, at microwave energies, with a new level of quantum control.