Recent connections in the adaptive control literature to continuous-time analogs of Nesterov's accelerated gradient method have led to the development of new real-time adaptation laws based on accelerated gradient methods. However, previous results assume that the system's uncertainties are linear-in-the-parameters (LIP). To compensate for non-LIP uncertainties, our preliminary results developed a neural network (NN)-based accelerated gradient adaptive controller to achieve trajectory tracking for nonlinear systems; however, the development and analysis only considered single-hidden-layer NNs. In this article, a generalized deep NN (DNN) architecture with an arbitrary number of hidden layers is considered, and a new DNN-based accelerated gradient adaptation scheme is developed to generate estimates of all the DNN weights in real-time. A nonsmooth Lyapunov-based analysis is used to guarantee the developed accelerated gradient-based DNN adaptation design achieves global asymptotic tracking error convergence for general nonlinear control affine systems subject to unknown (non-LIP) drift dynamics and exogenous disturbances. A comprehensive set of simulation studies are conducted on a two-state nonlinear system, a robotic manipulator, and a complex 20-D nonlinear system to demonstrate the improved performance of the developed method. Our simulation studies demonstrate enhanced tracking and function approximation performance from both DNN architectures and accelerated gradient adaptation.