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Low incidence rates of malaria (<1/1000 population at risk) in South Africa led the World Health Organization to recommend that the country pursue malaria elimination (zero local cases). The first elimination strategy published in 2012, targeted elimination by 2018. Unfortunately, this goal was not realised. This paper explores the challenges faced and lessons learnt during the implementation of the country's first elimination strategy and makes recommendations for accelerating towards malaria elimination using the revised elimination strategy (2019–2023). Secondary descriptive data analysis was used to gauge progress and identify challenges and lessons learnt. Data were sourced from the WHO malaria end term programme review reports (2012–2018), a WHO malaria elimination certification checklist report and the National Malaria DHIS2 malaria elimination database. Malaria cases in South Africa increased from 5255 in 2012 to 15,554 in 2018, with an outbreak in 2017 where 28,264 cases were reported. Local transmission occurred in 11 of the 52 districts but with varying transmission intensities. Sub-optimal coverage of essential vector control and surveillance interventions were noted in KwaZulu-Natal, Limpopo and Mpumalanga provinces. Case notification within 24 h, and accurate case classification remain challenges. The National Malaria Control Programme mobilised additional financial resources from government to address the challenges identified – particularly, in terms of vector control intervention coverage, surveillance activities (parasitological and entomological) and employment of an appropriately skilled workforce. Districts with close to zero local cases will be supported for sub-national malaria elimination. This phased approached will advance elimination of malaria in South Africa. [ABSTRACT FROM AUTHOR]