European Commission head Ursula von der Leyen also plans to mobilise a 4.7-billion-euro ($5 billion) investment package in South Africa that includes funding for a transition to clean energy and to boost vaccine manufacturing.
The EU-South Africa summit came at a time of "global uncertainty ... characterised by rising unilateralism, economic nationalism", South Africa's President Cyril Ramaphosa said in opening remarks that referenced a huge global shake-up since US leader Donald Trump took office.
There had been a retreat from "a world order that seeks to advance all nations" and promote a human rights culture, he said.
"If there ever was a time when it is absolutely necessary for partners who share the same values to work together, this is the time, particularly when multilateralism is under attack, particularly when the world order process is also being weakened," he said.
"This is the time to work together in defence of what we believe in, democracy, the rule of law, including the respect for international law and international humanitarian law."
Ramaphosa said the turmoil on the global stage would only serve to strengthen South Africa's relationship with the EU.
"What is going on in the world is even going to strengthen our resolve to remain partners in order to tackle the many challenges that are arising," he told reporters at the end of the summit that included European Council President Antonio Costa.
- 'Rules-based international order' -
Both South Africa and the EU are grappling with dramatic policy shifts from Washington since Trump return to the White House this year, including on commitments to combat global warming, trade and tariffs, and Russia's war in Ukraine.
Trump's government has criticised South African policies and frozen crucial aid.
It has also imposed tariffs of 25 percent on steel and aluminium imports from EU and on Thursday threatened to impose a 200 percent tariff on wine, champagne and other alcoholic products from the 27-nation bloc.
The United States has meanwhile pulled out of a climate funding deal to help developing countries transition to clean energy, one of the main beneficiaries of which is South Africa.
Von der Leyen said the massive EU investment package included funding for a transition to clean energy from the wind and sun and through the production of hydrogen.
It would also go towards ramping up vaccine manufacturing in South Africa, the continent's most industrialised economy and this year's president of the G20 grouping of leading economies.
"We know that others are withdrawing. So here we want to be very clear with our message: we are doubling down with our support and are here to stay," the EU chief said at the end of summit, describing a "new chapter" in relations.
"We stand for a rules-based international order and rule of law over the rule of force," she said.
The EU was also "100 percent behind" South Africa's G20 presidency which will culminate in the group's first summit on the continent in November, she said.
The United States did not send it top ministers to the first G20 ministers meetings in South Africa this year, complaining the agenda was "anti-American".
The summit also discussed efforts to end the war in Ukraine, with President Volodymyr Zelensky expected in South Africa next month. "We've been encouraging both Ukraine and Russia to find a peaceful solution," Ramaphosa said.
South Africa is the EU's largest trading partner in sub-Saharan Africa, exporting some 24 billion euros in goods in 2023, mostly minerals and automotive goods.
The trade deficit is nonetheless inclined in favour of the EU.
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