Early reports indicated a moderate turn-out for the sympathy strike but union leaders said it would intensify during the day.
Analysts say the strike, which began on June 1, has turned into a demonstration of labour power as the ruling African National Congress (ANC) prepares for a leadership assembly later this year.
Durban, a major port, was all but shut down as buses and taxis stopped operating. Activity was paralysed in hospitals, schools and public offices.
However, transport was still normal in Johannesburg, the country's economic centre, and a number of other cities.
The strike has forced the government to call in army medics to staff public hospitals.
Union leaders say tens of thousands of sympathy strikers will march in dozens of cities on Wednesday despite government warnings that police and army units are ready to respond to any violence.
Charles Nqakula, safety and security minister, said: "We are going to continue to deploy members of the South African police service, who will be assisted by units of the South African National Defence Force ... to deal with protection of all workers who want to go to work."
Public service unions are demanding a 10 per cent wage rise while the government of Thabo Mbeki, the South African president, counter offered with a 6.5 per cent increase. It has been suggested it may go as high as 7.25 per cent.
|About 30,000 workers strike in Durban [AFP]|
Workers in essential services such as the police, healthcare and emergency services personnel are barred by law from joining the strike.
Some Cosatu unions, including the powerful National Union of Mineworkers (NUM), have said they will not join the boycott because they have not had enough time to inform their members - a requirement by law.
But many other union groups said they were ready to turn out to support the civil servants.
Unions are pushing for a left-wing government when a new president takes office in 2009 - reflecting criticism that Mbeki's market-friendly policies have not done enough to help the black majority.
Jovial Rantao, a commentator for the Star newspaper, said on Wednesday: "This is the one strike aimed at Mbeki and his supporters."
"Once the strike is over, the unions would have demonstrated that they can, if they want to, bring the government and indeed the rest of the country to its knees."