Output-only modal parameter identification is based on the assumption that external forces on a linear structure are white noise. However, harmonic excitations are also often present in real structural vibrations. In particular, it has been realized that the use of forced acceleration responses without knowledge of external forces can pose a problem in the modal parameter identification, because an external force is imparted to its impulse acceleration response function. This paper provides a three-stage identification procedure as a solution to the problem of harmonic and white noise excitations in the acceleration responses of a linear dynamic system. This procedure combines the uses of the mode indicator function, the complex mode indication function, the enhanced frequency response function, an iterative rational fraction polynomial method and mode shape inspection for the correlation-related functions of the force-embedded acceleration responses. The procedure is verified via numerical simulation of a five-floor shear building and a two-dimensional frame and also applied to ambient vibration data of a large-span roof structure. Results show that the modal parameters of these dynamic systems can be satisfactorily identified under the requirement of wide separation between vibration modes and harmonic excitations.