The interaction between mixed autonomy traffic and public transport vehicles competing for limited road space is a less explored area of research. To evaluate the traffic dynamics in bimodal networks, a three-dimensional (passenger) network fundamental diagram, known as 3D-NFD (3D-pNFD), can be estimated that relates the accumulation of cars (autonomous and human-driven) and buses to the network vehicular (passenger) travel production. In this study, we propose a 3D-pNFD-based congestion pricing scheme considering three vehicle classes of buses, system-optimal (SO) seeking connected and automated vehicles (CAVs), and user-equilibrium (UE) seeking human-driven vehicles (HVs). We develop an iterative tri-level modeling framework for mode choice, pricing, and route choice in a mixed autonomy network. The lower level generates mixed equilibrium traffic flow through an integrated mixed equilibrium simulation-based dynamic traffic assignment model and a transit assignment model. The mid-level finds the optimal toll rates through a 3D-pNFD feedback-based controller. A nested logit-based mode choice model is also applied to capture travelers’ preferences toward three available modes and incorporates elastic demand. To encourage CAVs to follow the SO routing mode, they are provided with a discount on the congestion toll whereas UE-seeking HVs are subject to full price toll. Buses are also entirely exempt from the toll. We explore three scenarios with different discount rates on SO-seeking CAVs to investigate the effect of the incentive plans on the mode choice behaviors of road users in the pricing zone. The performance of the proposed model is evaluated in a large-scale network in Melbourne, Australia.