The work stoppage was led by one of South Africa's largest labor unions, the Public Servants Association (PSA), which has more than 235,000 members.
Member nurses, immigration workers and some police officers picketed outside the Treasury office in Pretoria waving black placards reading "public servants are bleeding."
Unions want a 6.5 percent hike. The increase weighs below South Africa's inflation which peaked at 7.8 percent in July.
The wage stalemate between the government and its employees escalated after Labor Minister Thulas Nxesi last week declared he would unilaterally implement a three percent increase across the board.
Finance Minister Enoch Godongwana said during his October mini-budget speech that government could only afford an average wage increase of 3.3 percent.
The PSA had warned on Wednesday that the strike would "have a serious impact" on the home affairs, transport and border control departments.
It said the minister's "irresponsible action has further damaged the already fragile relations and severe trust deficit" between government and unions.
Finance Minister Enoch Godongwana said during his October mini-budget speech that government could only afford an average wage increase of 3.3 percent.
South Africa's economy recently took a blow when workers at the state rail and port firm launched a weeks-long strike which left mineral and fresh fruit exports stranded.