The Naval Research Laboratory three-dimensional simulation code SAMI3/ESF is used to study the response of the post-sunset ionosphere to electrified mesoscale traveling ionospheric disturbances (MSTIDs). An MSTID is modeled as an externally-imposed traveling-wave E field with wavelength 250 km and period 1 h that drives vertical E × B drifts of up to ±50 m/s. We find that the coupling between the MSTID at low- to mid-latitudes and the equatorial F layer leads to growth of equatorial plasma bubbles (EPBs). This coupling is strongest when the wave vector is perpendicular to the geomagnetic field. Model results reproduce key features of observed nighttime MSTIDs and associated EPBs.