Topological quantum computation encodes quantum information nonlocally by nucleating non-Abelian anyons separated by distances $L$, typically spanning the qubit device size. This nonlocality renders topological qubits exponentially immune to dephasing from all sources of classical noise with operator support local on the scale of $L$. We perform detailed analytical and numerical analyses of a time-domain Ramsey-type protocol for noisy Majorana-based qubits that is designed to validate this coveted topological protection in near-term devices such as the so-called `tetron design. By assessing dependence of dephasing times on tunable parameters, e.g., magnetic field, our proposed protocol can clearly distinguish a bona fide Majorana qubit from one constructed from semilocal Andreev bound states, which can otherwise closely mimic the true topological scenario in local probes. In addition, we analyze leakage of the qubit out of its low-energy manifold due to classical-noise-induced generation of quasiparticle excitations; leakage limits the qubit lifetime when the bulk gap collapses, and hence our protocol further reveals the onset of a topological phase transition. This experiment requires measurement of two nearby Majorana modes for both initialization and readout---achievable, for example, by tunnel coupling to a nearby quantum dot---but no further Majorana manipulations, and thus constitutes an enticing pre-braiding experiment. Along the way, we address conceptual subtleties encountered when discussing dephasing and leakage in the context of Majorana qubits.
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