"The idea is that the countries support South Africa to phase out of coal faster and to go earlier and faster into developing renewables. We're still working on that," von der Leyen told a news conference, adding that the US, the UK, Germany and France were also involved.
EU sources said the partnership would focus on a "just transition" in South Africa, by providing support to the regions and workers in coal industries that would be affected by a phaseout.
Coal-fuelled plants supplied nearly 90% of South Africa's electricity last year.
Ursula Von der Leyen also said 60 countries have now joined a pledge led by the EU and United States to cut methane emissions.
The pledge, which will also be launched at the COP26 summit, would see countries commit to slash their joint methane emissions by 30% by 2030 from 2020 levels.
Nigeria, Japan and Pakistan are among the countries that have signed up.
The initiative is to be launched at the COP26 climate summit from 31 October to 12 November in Glasgow, Scotland.
Coal is the most polluting fossil fuel and phasing it out quickly is seen as crucial if the world is to meet the Paris Agreement's target to limit global warming to 1.5⁰C and avert the most catastrophic impacts of climate change.
Methane is the second-biggest cause of climate change after carbon dioxide.
The gas has a higher heat-trapping potential than CO2 but it breaks down in the atmosphere faster, meaning deep cuts in methane emissions could have a rapid impact on slowing global warming.
The aim of the Glasgow summit is to secure enough new commitments and deals from countries and polluting industries to cut emissions fast enough to keep the 1.5⁰C target within reach.
U.N. secretary general, Antonio Guterres, has called on all rich countries to stop burning coal by 2030, and for poorer countries to do so by 2040.
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