A single spin in a Josephson junction can reverse the flow of the supercurrent. At mesoscopic length scales, such $pi$-junctions are employed in various instances from finding the pairing symmetry to quantum computing. In Yu-Shiba-Rusinov (YSR) states, the atomic scale counterpart of a single spin in a superconducting tunnel junction, the supercurrent reversal so far has remained elusive. Using scanning tunneling microscopy (STM), we demonstrate such a 0 to $pi$ transition of a Josephson junction through a YSR state as we continuously change the impurity-superconductor coupling. We detect the sign change in the critical current by exploiting a second transport channel as reference in analogy to a superconducting quantum interference device (SQUID), which provides the STM with the required phase sensitivity. The measured change in the Josephson current is a signature of the quantum phase transition and allows its characterization with unprecedented resolution.
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