pi-phase shifters fabricated using well-established Nb-based technology of superconductor-ferromagnet-superconductor Josephson junctions. The important feature here is to obtain high interface transparency between Nb and Al layers without degrading sub-micron shadow mask. We achieve this by in-situ Ar etching using e-beam gun. Shadow-evaporated Al/AlOx/Al Josephson junctions with Nb bias pads show the expected current-voltage characteristics with reproducible critical currents. Using this technique, we fabricated composite Nb/Al flux qubits with Nb/CuNi/Nb pi-shifters and measured their magnetic field response. The observed offset between the field responses of the qubits with and without pi-junction is attributed to the pi phase shift. The reported approach can be used for implementing a variety of hybrid Nb/Al superconducting quantum circuits.