Measuring the geometry of multi-planet extrasolar systems can provide insight into their dynamical history and the processes of planetary formation. Such measurements are challenging for systems detected through indirect techniques such as radial velocity and transit, having only been measured for a handful of systems to-date. We aimed to place constraints on the orbital geometry of the outer planet in the $pi$ Mensae system, a G0V star at 18.3 pc host to a wide-orbit super-jovian ($Msin i = 10.02pm0.15$ $M_{rm Jup}$) with a 5.7-year period and an inner transiting super-earth ($M=4.82pm0.85$ $M_oplus$) with a 6.3-d period. We combined astrometric measurements from the Hipparcos and Gaia satellites with a precisely determined spectroscopic orbit in an attempt to constrain the inclination of the orbital plane of the outer planet. We measured an inclination of $i_b=49.9_{-4.5}^{+5.3}$ deg for the orbital plane of $pi$ Mensae b, leading to a direct measurement of its mass of $13.01_{-0.95}^{+1.03}$ $M_{rm Jup}$. We found a significant mutual inclination between the orbital planes of the two planets; a 95% credible interval for $i_{rm mut}$ of between $34.5^circ$ and $140.6^circ$ after accounting for the unknown position angle of the orbit of $pi$ Mensae c, strongly excluding a co-planar scenario for the two planets within this system. All orbits are stable in the present-day configuration, and secular oscillations of planet cs eccentricity are quenched by general relativistic precession. Planet c may have undergone high eccentricity tidal migration triggered by Kozai-Lidov cycles, but dynamical histories involving disk migration or in situ formation are not ruled out. Nonetheless, this system provides the first direct evidence that giant planets with large mutual inclinations have a role to play in the origins and evolution of some super-Earth systems.