We report on the precise integration of nm-scale topological insulator Josephson junctions into mm-scale superconducting quantum circuits via selective area epitaxy and local stencil lithography. By studying dielectric losses of superconducting microwave resonators fabricated on top of our selective area growth mask, we verify the compatibility of this in situ technique with microwave applications. We probe the microwave response of on-chip microwave cavities coupled to topological insulator-shunted superconducting qubit devices and observe a power dependence that indicates nonlinear qubit behaviour. Our method enables integration of complex networks of topological insulator nanostructures into superconducting circuits, paving the way for both novel voltage-controlled Josephson and topological qubits.