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Routing controllability of connected and autonomous vehicles (CAVs) has been shown to reduce the adverse effects of selfish routing on the network efficiency. However, the assumption that CAV owners would readily allow themselves to be controlled externally by a central agency for the good of the system is unrealistic. In this paper, we propose a joint routing and pricing control scheme that aims to incentivize CAVs to seek centrally controlled system-optimal (SO) routing by saving on tolls while user equilibrium (UE) seeking human-driven vehicles (HVs) are subject to a congestion charge. The problem is formulated as a bi-level optimization program where the upper level optimizes the dynamic toll rates using the network fundamental diagram (NFD) and the lower level is a mixed equilibrium simulation-based dynamic traffic assignment model (SBDTA) considering different combinations of SO-seeking CAVs. We apply a feedback-based controller to solve for the optimal spatially differentiated distance-based congestion charge from which SO-seeking CAVs are exempt; but UE-seeking HVs are subject to the charge for entering the city center. To capture the distinct microscopic behavior of CAVs in the mixed autonomy traffic, we also implement an adaptive link fundamental diagram (FD) within the SBDTA model. The proposed joint control scheme encourages CAV owners to seek SO routing resulting in less total system travel time. It also discourages UE-seeking HVs from congesting the city center. We demonstrate the performance of the proposed scheme in both a small network and a large-scale network of Melbourne, Australia.