Hybrid quantum registers, such as electron-nuclear spin systems, have emerged as promising hardware for implementing quantum information and computing protocols in scalable systems. Nevertheless, the coherent control of such systems still faces challenges. Particularly, the lower gyromagnetic ratios of the nuclear spins cause them to respond slowly to control fields, resulting in gate times that are generally longer than the coherence time of the electron spin. Here, we demonstrate a scheme for circumventing this problem by indirect control: We apply a small number of short pulses only to the electron spin and let the full system undergo free evolution under the hyperfine coupling between the pulses. Using this scheme, we realize robust quantum gates in an electron-nuclear spin system, including a Hadamard gate on the nuclear spin and a controlled-NOT gate with the nuclear spin as the target qubit. The durations of these gates are shorter than the electron spin coherence time, and thus additional operations to extend the system coherence time are not needed. Our demonstration serves as a proof of concept for achieving efficient coherent control of electron-nuclear spin systems, such as NV centers in diamond. Our scheme is still applicable when the nuclear spins are only weakly coupled to the electron spin.