This investigation presents observations related to the generation of equatorial ionospheric irregularities (also known as equatorial spread F (ESF)) including ionospheric plasma bubbles and dynamic behavior of the ionospheric F-region in the South American sector during an intense geomagnetic storm in December 2006 (a period of low solar activity). In this work, ionospheric sounding observations and GPS data obtained between 13 and 16 December 2006 at several stations in the South American sector are presented. On the geomagnetically disturbed night of 14 and 15 December, ionospheric plasma bubbles were observed after an unusual uplifting of the F-region during pre-reversal enhancement (PRE) period. The unusual uplifting of the F-region during PRE was possibly associated with prompt penetration of electric field of magnetospheric origin. During the geomagnetic disturbance night of 14 and 15 December, strong oscillations due to the propagation of traveling ionospheric disturbances (TIDs) by the Joule heating in the auroral region were observed in the F-region at São José dos Campos (SJC, 23.2°S, 45.9°W; dip latitude 17.6°S), Brazil, and Port Stanley (PST, 51.6°S, 57.9°W; geom. latitude 41.6°S). The VTEC-GPS observations presented on the night of 14 and 15 December 2006 show both positive and negative storm phases in the South American sector, possibly due to changes in the large-scale wind circulation and changes in the O/N2 ratio in the southern hemisphere, respectively.