Given the difficulty of accurately measuring external inputs acting on structures, the research on joint input-system identification has gained significant attention in recent years. Among them, several unscented Kalman filters under unknown input (UKF-UI) based methods have been proposed for joint input and system identification. However, the existing UKF-UI methods require unknown inputs to be presented in the observation equations, which is not always available in practical engineering. To solve this problem, an unscented Kalman filter under unknown input without direct feedthrough (UKF-UI-WDF) is proposed in this paper for real-time joint input and system identification of structural systems without direct feedthrough using limited response measurements. The proposed UKF-UI-WDF is derived for recursive identification of the structural states, parameters, and unknown inputs by integrating unknown input estimation into the conventional UKF framework. In each identification step, the unknown inputs are first identified by minimizing posterior residuals of measurements, and then the structural states and parameters are identified by a traditional unscented Kalman filtering using the identified unknown inputs. According to whether the uncertainty of the identified unknown inputs can be quantitatively described or not, two implementation algorithms are provided in this paper. In algorithm 1, only the mean values of unknown inputs can be identified. In algorithm 2, the unknown inputs are identified as a set of sigma points, so not only the mean values but also the variance of the unknown inputs can be estimated. The effectiveness of the proposed method is examined by the joint input and system identification of various case studies of linear and nonlinear hysteretic shear structures subjected to unknown external or base excitations, respectively. The results show that the proposed UKF-UI-WDF method can effectively perform real-time joint input-system identification of structural systems without direct feedthrough using limited response measurements.