Experimental and numerical analyses were carried out in order to identify damage in metal-composite bonded joints, which were manufactured from carbon-fiber reinforced polymers and titanium plates joined by an epoxy resin. The monitoring was performed by using vibration-based method through changes in frequency response function (FRF). First, free-free vibration tests were performed on four different specimens (with presence or not of damage and with presence or not piezoelectric sensor). Finite element analyses for the conditions without the transducer were also carried out and compared with the experimental data. FRFs were obtained by using the response of the PZT placed over the titanium plate and accelerometers located at other positions of the joint. The damage was reproduced by replacing 50% of the overlap with a layer of Teflon. Lastly, based on damage identification metric, FRFs for the undamaged and damaged structure were compared, evaluating not only the potentialities and limitations of the applied experimental detection technique, but also the computational model. The experimental and numerical results showed that the vibration-based damage identification methods combined to the metrics can be used in structural health monitoring systems.