The diminishing strength of the Earth’s magnetic dipole over recent millennia is accompanied by the increasing prominence of the geomagnetic South Atlantic Anomaly (SAA), which spreads over the South Atlantic Ocean and South America. The longevity of this feature at millennial timescales is elusive because of the scarcity of continuous geomagnetic data for the region. Here, we report a unique geomagnetic record for the last ∼1500 y that combines the data of two well-dated stalagmites from Pau d’Alho cave, located close to the present-day minimum of the anomaly in central South America. Magnetic directions and relative paleointensity data for both stalagmites are generally consistent and agree with historical data from the last 500 y. Before 1500 CE, the data adhere to the geomagnetic model ARCH3K.1, which is derived solely from archeomagnetic data. Our observations indicate rapid directional variations (>0.1°/y) from approximately 860 to 960 CE and approximately 1450 to 1750 CE. A similar pattern of rapid directional variation observed from South Africa precedes the South American record by 224 ± 50 y. These results confirm that fast geomagnetic field variations linked to the SAA are a recurrent feature in the region. We develop synthetic models of reversed magnetic flux patches at the core–mantle boundary and calculate their expression at the Earth’s surface. The models that qualitatively resemble the observational data involve westward (and southward) migration of midlatitude patches, combined with their expansion and intensification.