Quantum anomalies are violations of classical scaling symmetries caused by divergences that appear in the quantization of certain classical theories. Although they play a prominent role in the quantum field theoretical description of many-body systems, their influence on experimental observables is difficult to discern. In this study, we discovered a distinctive manifestation of a quantum anomaly in the momentum-space dynamics of a two-dimensional (2D) Fermi superfluid of ultracold atoms. The measured pair momentum distributions of the superfluid during a breathing mode cycle exhibit a scaling violation in the strongly interacting regime. We found that the power-law exponents that characterize long-range phase correlations in the system are modified by the quantum anomaly, emphasizing the influence of this effect on the critical properties of 2D superfluids.