Police in Pretoria opened fire with rubber bullets on an illegal gathering of striking truck drivers on Wednesday morning.
The protestors have demanded a 13 percent wage increase. They also want the minimum salary for long-distance truckers to be pushed up to R6000.
There have been reports of intimidation in Ekurhuleni, the Johannesburg city centre and Pretoria.
Police fired rubber bullets after the protestors became unruly. But the situation has calmed.
The demonstrators have insisted the protest was not an illegal gathering but the Tshwane Metro Council maintains no permission was given for the demonstration.
Elsewhere in the capital, three trucks were set alight east of Pretoria, while two others were torched on the opposite end of the city on Tuesday night.
The South African Transport and Allied Workers Union has denied allegations that its members were involved in these acts of intimidation, saying their protest was a peaceful one.
There concerns that if the strike carries on through the long weekend petrol stations across the country could run dry because there will be few or no drivers available to transport fuel.