We experimentally constructed an all-microwave scheme for the controlled-NOT (cNOT) gate between two superconducting transmon qubits in a three dimensional cavity. Our cNOT gate is based on the microwave-activated phase (MAP) gate, which requires an additional procedure to compensate the accumulated phases during the operation of the MAP gate. We applied Z-axis phase gates using microwave hyperbolic secant pulse on both qubits with adequate rotation angles systematically calibrated by separate measurements.We evaluated the gate performance of the constructed cNOT gate by performing two-qubit quantum process tomography (QPT). Finally, we present the experimental implementation of Deutsch-Jozsa algorithm using the cNOT gate.