Chanting “Cyril must go,” they held up signs demanding a wage increase during a ceremony in a stadium near the north-western city of Rustenburg.
The protesters, who worked at a local mine, have been striking for weeks.
President Ramaphosa tried to address the miners’ concerns but was greeted by booing.
The workers want an annual salary pay rise of 1,000 rand ($63; £50) – a demand which President Ramaphosa addressed directly.
“We have heard that message and we will be dealing with that matter,” he is quoted as telling the miners by the IOL news site.
He also pledged to speak to the relevant authorities to meet their demands, IOL reports.
In a two-minute video of the disruption, the president can be seen making repeated attempts to calm the workers down, only to be greeted with further jeering and booing.
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At Sunday’s event, which had been organised by South Africa’s trade union federation Cosatu, police had to step in while a bodyguard led the president away from the venue, according to IOL.
The workers were from Sibanye-Stillwater, which is a metal mining company and the world’s largest primary producer of platinum, according to its own website.
South Africa’s economy has been hit hard by the Covid crisis, and unemployment is now around 35%.
Mining is one of South Africa’s most important sectors – accounting for 8-10% of national income and employing almost 450,000 people – but it has been in decline in recent years.
Analysis by Lebo Diseko, BBC News, Johannesburg
May Day is a key event in the yearly calendar of the ruling African National Congress (ANC) and its trade union allies, and usually draws huge crowds. The fact that what looked like just a few hundred workers turned out to see the president speak was an indication that he was not welcome.
Questions are now being asked about how and why security assessments did not pick up that this might happen.
But perhaps the more important question is why the ANC and Cosatu leaders seem to have been surprised at the level of anger on the ground. It suggests a level of disconnect between the experiences of ordinary people, and those in power.
It is worth noting that some of those who jeered President Ramaphosa at the rally were members of the union he helped to found. Mr Ramaphosa was the first general secretary of the National Union of Mineworkers.
This is a year in which the ANC holds elections which will decide who leads the party into the country’s next general election. This sort of reception from a key constituency – workers – may foreshadow some of the challenges Mr Ramaphosa could face in seeking re-election.