A novel two-loop structured robust generalized dynamic inversion-based control system is proposed for autonomous underwater vehicles. The outer (position) loop of the generalized dynamic inversion control system utilizes proportional-derivative control of the autonomous underwater vehicle's inertial position errors from the desired inertial position trajectories, and it provides the reference yaw and pitch attitude angle commands to the inner loop. The inner (attitude) loop utilizes generalized dynamic inversion control of a prescribed asymptotically stable dynamics of the attitude angle errors from their reference values, and it provides the required control surface deflections such that the desired inertial position trajectories of the vehicle are tracked. The dynamic inversion singularity is avoided by augmenting a dynamic scaling factor within the Moore-Penrose generalized inverse in the particular part of the generalized dynamic inversion control law. The involved null control vector in the auxiliary part of the generalized dynamic inversion control law is constructed to be linear in the pitch and yaw angular velocities, and the proportionality gain matrix is designed to guarantee global closed-loop asymptotic stability of the vehicle's angular velocity dynamics. An additional sliding mode control element is included in the particular part of the generalized dynamic inversion control system, and it works to robustify the closed-loop system against tracking performance deterioration due to generalized inversion scaling, such that semi-global practically stable attitude tracking is guaranteed. A detailed six degrees-of-freedom mathematical model of the Monterey Bay Aquarium Research Institute autonomous underwater vehicle is used to evaluate the control system design, and numerical simulations are conducted to demonstrate closed-loop system performance under various types of autonomous underwater vehicle maneuvers, under both nominal and perturbed autonomous underwater vehicle system's mathematical model parameters.