Dephasing -- phase randomization of a quantum superposition state -- is a major obstacle for the realization of high fidelity quantum logic operations. Here, we implement a two-qubit Controlled-NOT gate using dynamical decoupling (DD), despite the gate time being more than one order of magnitude longer than the intrinsic coherence time of the system. For realizing this universal conditional quantum gate, we have devised a concatenated DD sequence that ensures robustness against imperfections of DD pulses that otherwise may destroy quantum information or interfere with gate dynamics. We compare its performance with three other types of DD sequences. These experiments are carried out using a well-controlled prototype quantum system -- trapped atomic ions coupled by an effective spin-spin interaction. The scheme for protecting conditional quantum gates demonstrated here is applicable to other physical systems, such as nitrogen vacancy centers, solid state nuclear magnetic resonance, and circuit quantum electrodynamics.
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