We present the software system used to control and operate the South Pole Telescope. The South Pole Telescope is a 10-meter millimeter-wavelength telescope designed to measure anisotropies in the cosmic microwave background (CMB) at arcminute angular resolution. In the austral summer of 2011/12, the SPT was equipped with a new polarization-sensitive camera, which consists of 1536 transition-edge sensor bolometers. The bolometers are read out using 36 independent digital frequency multiplexing (DfMux) readout boards, each with its own embedded processors. These autonomous boards control and read out data from the focal plane with on-board software and firmware. An overall control software system running on a separate control computer controls the DfMux boards, the cryostat and all other aspects of telescope operation. This control software collects and monitors data in real-time, and stores the data to disk for transfer to the United States for analysis.