In this paper, we investigate signatures of topological phase transitions in interacting systems. We show that the key signature is the existence of a topologically protected level crossing, which is robust and sharply defines the topological transition, even in finite-size systems. Spatial symmetries are argued to play a fundamental role in the selection of the boundary conditions to be used to locate topological transitions in finite systems. We discuss the theoretical implications of these results, and utilize exact diagonalization to demonstrate its manifestations in the Haldane-Fermi-Hubbard model. Our findings provide an efficient way to detect topological transitions in experiments and in numerical calculations that cannot access the ground-state wave function.