Robust control systems are a necessity for autonomous underwater vehicle (AUV) systems due to the challenges they face during operation. Many AUV control-design methods have been developed for different actuator configurations, with robustness against model parameter uncertainties, environmental disturbances, and system faults. Actuator faults can reduce the physical capabilities of a system, which can be compensated for through control re-allocation. However, the increased control allocation to the remaining actuators may cause actuator saturation and reduce controller performance. In this work, we present a depth-pitch model-based nonlinear control law that directly considers actuator saturation, and a fault-tolerant control allocation method for a hybrid AUV actuator configuration. Two types of actuator faults are considered for an underwater vehicle with a hybrid actuator configuration. The proposed controller is implemented in a simulated system, and its trajectory tracking performance is compared with a baseline system without fault or saturation tolerance. To determine the utility of the proposed saturation and fault tolerance control methods, the tracking performance in these simulations is quantified in terms of the settling time, post-fault peak values, and root mean square of the depth and pitch errors.