This paper proposes a Prony-based parallel two-stage method for delay-Doppler estimation in OTFS systems. By performing delay-first and Doppler-first estimations in parallel and fusing the results, the method resolves ambiguities caused by similar path characteristics. The simulation results demonstrate the superior accuracy and robustness of the proposed method under various conditions. This method provides a promising solution for future applications such as Vehicle-to-Vehicle (V2V) and Integrated Sensing and Communication (ISAC).