Universal quantum computers require fault-tolerant logical qudits, as qudits naturally align with the simulation of multi-level physical systems. Here, we present a general framework and working examples for encoding fault-tolerant logical qudits in finite-dimensional spin systems. We construct distance-3, distance-5 codewords, and general 2t+1-distance codes that can be implemented using a single physical qudit or a small number of coupled qudits for higher distances, while requiring a Hilbert space dimension significantly smaller than conventional constructions based on multiple logical qubits. Logical operations and error correction protocols can be implemented with polynomial scaling in the number of elementary operations. We further discuss schematic designs for physical implementation and required single-gate fidelities, which are compatible with current spin qudit platforms. This strategy provides a resource-efficient path toward realizing fault-tolerant logical qudits in finite multi-level physical systems.