In optimal quantum control, control landscape phase transitions (CLPTs) indicate sharp changes occurring in the set of optimal protocols, as a physical model parameter is varied. Here, we demonstrate the existence of a new class of CLPTs, associated with changes in the topological properties of the optimal level set in a two-qubit state-preparation problem. In particular, the distance distribution of control protocols sampled through stochastic homotopic dynamics reveals discontinuous changes in the number of connected components in the optimal level set, as a function of the protocol duration. We demonstrate how topological CLPTs can be detected in modern-day experiments.