Green hydrogen projects use renewable energy to split water into hydrogen and oxygen, making fuel that can be used across industries such as transport, petrochemicals and steel.
The first EU grant, worth 140 million rand ($7.8 million), is to help struggling South African state company Transnet with infrastructure costs, supporting railways, ports, pipelines and other logistics.
The other grant, for 25 million euros ($27.6 million), will help Africa's most industrialised economy develop its green hydrogen value chain.
Green hydrogen is seen as critical to decarbonisation efforts in South Africa and Europe.
European countries have been investing in green hydrogen projects across Africa to secure future supplies of the fuel.
"These two European Union grants will be implemented in a way so that they contribute to South Africa's strategic objectives," Kadri Simson, European commissioner for energy, told reporters in Pretoria, South Africa's administrative capital.
"We think that green hydrogen provides some of the best opportunities for the country to really industrialise," said Kgosientsho Ramokgopa, South Africa's minister of energy and electricity.
