Herein, two novel Physics Informed Neural Network (PINN) architectures are proposed for output-only system identification and input estimation of dynamic systems. Using merely sparse output-only measurements, the proposed PINNs architectures furnish a novel approach to input, state, and parameter estimation of linear and nonlinear systems with multiple degrees of freedom. These architectures are comprised of parallel and sequential PINNs that act upon a set of ordinary differential equations (ODEs) obtained from spatial discretization of the partial differential equation (PDE). The performance of this framework for dynamic system identification and input estimation was ascertained by extensive numerical experiments on linear and nonlinear systems. The advantage of the proposed approach, when compared with system identification, lies in its computational efficiency. When compared with traditional Artificial Neural Networks (ANNs), this approach requires substantially smaller training data and does not suffer from generalizability issues. In this regard, the states, inputs, and parameters of dynamic state-space equations of motion were estimated using simulated experiments with “noisy” data. The proposed framework for PINN showed excellent great generalizability for various types of applications. Furthermore, it was found that the proposed architectures significantly outperformed ANNs in generalizability and estimation accuracy.