This study has developed a new TEC‐based ionospheric data assimilation system for 3‐D regional ionospheric imaging over the South American sector (TIDAS‐SA) (45°S–15°N, 35°–85°W, and 100–800 km). The TIDAS‐SA data assimilation system utilizes a hybrid Ensemble‐Variational approach to incorporate a diverse set of ionospheric data sources, including dense ground‐based Global Navigation Satellite System (GNSS) line‐of‐sight Total Electron Content (TEC) data, radio occultation data from the Constellation Observing System for Meteorology, Ionosphere, and Climate‐2 (COSMIC‐2), and altimeter TEC data from the JASON‐3 satellite. TIDAS‐SA can produce a reanalyzed three‐dimensional (3‐D) electron density spatial variation with a high time cadence, yielding spatial‐temporal resolution of 1° (latitude) × 1° (longitude) × 20 km (altitude) × 5 min. This allows us to reconstruct and study the 3‐D ionospheric morphology with multi‐scale structures. The performance of the data assimilation system is validated against independent ionosonde and in situ measurements through an experiment for a strong geomagnetic storm event on 03–04 November 2021. The results demonstrate that TIDAS‐SA can provide detailed and altitude‐resolved information that accurately characterizes the storm‐time ionospheric disturbances in vertical and horizontal domains over the equatorial and low‐latitude regions of South America.