Testing general relativity in the nonlinear, dynamical, strong-field regime of gravity is one of the major goals of gravitational wave astrophysics. Performing precision tests of general relativity (GR) requires numerical inspiral, merger, and ringdown waveforms for binary black hole (BBH) systems in theories beyond GR. Currently, GR and scalar-tensor gravity are the only theories amenable to numerical simulations. In this article, we present a well-posed perturbation scheme for numerically integrating beyond-GR theories that have a continuous limit to GR. We demonstrate this scheme by simulating BBH mergers in dynamical ChernSimons gravity (dCS), to linear order in the perturbation parameter. We present mode waveforms and energy fluxes of the dCS pseudoscalar field from our numerical simulations. We find good agreement with analytic predictions at early times, including the absence of pseudoscalar dipole radiation. We discover new phenomenology only accessible through numerics: a burst of dipole radiation during merger. We also quantify the self-consistency of the perturbation scheme. Finally, we estimate bounds that GR-consistent LIGO detections could place on the new dCS length scale, approximately l ≲ Oð10Þ km.