Despite intensive efforts to increase vaccine coverage, South Africa still has a low vaccination rate for coronavirus disease 2019 (COVID-19) in the African region. A comprehensive evaluation of the current vaccine promotion programs is urgently needed to guide policymakers to develop effective tailored programs. Geoadditive models were used to investigate the geospatial variations in correlates of vaccine hesitancy in South Africa. We used consecutive rounds of “COVID-19 Vaccine Surveys” (CVACS 1, n = 3510 and CVACS 2, n = 3608), which were implemented in 2021–22. We observed a considerable reduction in vaccine acceptability within less than 3 months. The model predicted degrees of freedom ranged from 4.13 to 12.66 and provided compelling evidence for sub-geographical level variations in vaccine hesitancy across the country. Our data visualization analysis showed strong geospatial correlations between vaccine hesitancy and beliefs. We found that most vaccine hesitancy could be avoided by increasing trust in the vaccine and the government. Investigating geospatial heterogeneity in correlates of vaccine acceptability may assist in modifying the current vaccine promotion strategies by targeting those who are vaccine hesitant due to unjustified/wrong rumors.