This study introduces a measurement technique for simultaneous phase-separated velocity in two-phase bubbly flow. The non-invasive technique, based on an Ultrasonic Velocity Profiler (UVP), is used in order to obtain an instantaneous, separate velocity profile for both liquid and bubble. The aim of this paper is to measure each phase velocity at the same time and position it using only a single resonant frequency. To achieve this aim, extended signal processing of the Short-Time Fourier Transform (STFT) is proposed, combining with amplitude classification to analyze Doppler signal influenced from the bubbly flow. The use of developed algorithms allows the instantaneous separation of liquid and bubble velocity profiles. In this work, the developed technique is used to measure the velocity profile of bubbly flow in the vertical pipe, demonstrating the classification of liquid and bubble velocity. To confirm the accuracy of each velocity profile phase, the Particle Image Velocimetry (PIV) method is used for comparison. The results clarify that the proposed method is in good agreement with the PIV measurement. Finally, the effect of void fraction against velocity measurement of both phases was demonstrated.