We produce the first numerical relativity binary black hole gravitational waveforms in a higher-curvature theory beyond general relativity. In particular, we study head-on collisions of binary black holes in order-reduced dynamical Chern-Simons gravity. This is a precursor to producing beyond-general-relativity waveforms for inspiraling binary black hole systems that are useful for gravitational wave detection. Head-on collisions are interesting in their own right, however, as they cleanly probe the quasi-normal mode spectrum of the final black hole. We thus compute the leading-order dynamical Chern-Simons modifications to the complex frequencies of the post-merger gravitational radiation. We consider equal-mass systems, with equal spins oriented along the axis of collision, resulting in remnant black holes with spin. We find modifications to the complex frequencies of the quasi-normal mode spectrum that behave as a power law with the spin of the remnant, and that are not degenerate with the frequencies associated with a Kerr black hole of any mass and spin. We discuss these results in the context of testing general relativity with gravitational wave observations.