We theoretically demonstrate the universal two-qubit CNOT gate between an ionic and an atomic qubit relying on Rydberg excitation of the atom and the resulting phonon blockade in the motional states of the harmonically trapped ion. The phonon blockade arises due to strong ion-atom interaction when the atom is excited to a Rydberg state. For realistic parameters, the gate fidelity is found to be about 90%. In a previous paper [S. Mudli {\it et al.} Phys. Rev. A 110, 062618 (2024)], it was shown that a trapped ion can mediate interaction between two largely separated Rydberg atoms, and this mediated interaction can be leveraged to perform a universal two-qubit gate operation between neutral atom qubits in optical tweezers. These demonstrations suggest that an ion-atom hybrid system can serve as a resourceful platform or module for quantum computing and quantum networking as it can utilize the best features of charged as well as neutral atom qubits. Finally, we discuss how to achieve higher gate fidelity by extending our proposed protocol and operating in a different parameter regime.