"The EU isn't asking South Africa to choose sides, just asking countries across the world to stand with the UN Charter," said Borrell, speaking alongside South Africa's foreign minister Naledi Pandor in the capital Pretoria.
The EU considers South Africa an important partner in the rules-based international order, he added.
Pandor said: "It is not just South Africa and other African countries that must play a role at seeking peace."
Russian Foreign Minister Sergei Lavrov visited South Africa recently, including with FM Pandor, who responded warmly in public to the engagement.
The two nations, along with China, plan joint naval drills soon.