The call signals an effort by the authorities in Pretoria to invigorate negotiations on a new trade deal with its biggest partner after China. The two nations have failed to make substantive progress on an accord since their leaders met at the White House in May.
Their call on Wednesday coincided with a meeting between South Africa's foreign minister, Ronald Lamola, and US charge d'affaires David Greene - currently the top US diplomat in Pretoria. Trump and Ramaphosa plan further talks, South Africa's presidency said in a statement on Thursday.
"The two leaders undertook to continue with further engagements recognising the various trade negotiations the US is currently involved in," it said. "Respective trade negotiating teams will take forward more detailed discussions."
The US imposed 30 tariffs on imports from South Africa, the highest duty charged on goods from any sub-Saharan African nation, as part of a shake-up of its relationship with its trading partners.