We demonstrate a SWAP gate between laser-cooled ions in a segmented microtrap via fast physical swapping of the ion positions. This operation is used in conjunction with qubit initialization, manipulation and readout, and with other types of shuttling operations such as linear transport and crystal separation and merging. Combining these operations, we perform quantum process tomography of the SWAP gate, obtaining a mean process fidelity of 99.5(5)%. The swap operation is demonstrated with motional excitations below 0.05(1)~quanta for all six collective modes of a two-ion crystal, for a process duration of 42~$mu$s. Extending these techniques to three ions, we reverse the order of a three-ion crystal and reconstruct the truth table for this operation, resulting in a mean process fidelity of 99.96(13)% in the logical basis.
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