Unexpected faults in actuators and sensors may degrade the reliability and safety of aero engineering systems. Therefore, there is motivation to develop integrated fault tolerant control techniques with applications to aero engineering systems. In this paper, discrete-time dynamic systems, in the presence of simultaneous actuator/sensor faults, partially decoupled unknown input disturbances, and sensor noises, are investigated. A jointly state/fault estimator is formulated by integrating an unknown input observer, augmented system approach, and optimization algorithm. Unknown input disturbances can be either decoupled by an unknown input observer, or attenuated by a linear matrix inequality optimization, enabling the estimation error to be input-to-state stable. Estimator-based signal compensation is then implemented to mitigate adverse effects from the unanticipated actuator and sensor faults. A pre-designed controller, which maintains normal system behaviors under a fault-free scenario, is allowed to work along with the presented fault tolerant mechanism of the signal compensations. The fault-tolerant closed-loop system can be ensured to mitigate the effects from the faults, guarantee the input-to-state stability, and satisfy the required robustness performance. The proposed fault estimation and fault tolerant control methods are developed for both discrete-time linear and discrete-time Lipschitz nonlinear systems. Finally, the proposed techniques are applied to a jet engine system and a flight control system for simulation validation.