Precision control over hybrid physical systems at the quantum level is important for the realization of many quantum-based technologies. In the field of quantum information processing (QIP) and quantum networking, various proposals discuss the possibility of hybrid architectures where specific tasks are delegated to the most suitable subsystem. For example, in quantum networks, it may be advantageous to transfer information from a subsystem that has good memory properties to another subsystem that is more efficient at transporting information between nodes in the network. For trapped ions, a hybrid system formed of different species introduces extra degrees of freedom that can be exploited to expand and refine the control of the system. Ions of different elements have previously been used in QIP experiments for sympathetic cooling, creation of entanglement through dissipation, and quantum non-demolition measurement of one species with another. Here we demonstrate an entangling quantum gate between ions of different elements which can serve as an important building block of QIP, quantum networking, precision spectroscopy, metrology, and quantum simulation. A geometric phase gate between a 9Be+ ion and a 25Mg+ ion is realized through an effective spin-spin interaction generated by state-dependent forces induced with laser beams. Combined with single-qubit gates and same-species entangling gates, this mixed-element entangling gate provides a complete set of gates over such a hybrid system for universal QIP. Using a sequence of such gates, we demonstrate a CNOT (controlled-NOT) gate and a SWAP gate. We further demonstrate the robustness of these gates against thermal excitation and show improved detection in quantum logic spectroscopy. We also observe a strong violation of a CHSH (Clauser-Horne-Shimony-Holt)-type Bell inequality on entangled states composed of different ion species.