Political analysts say the public service strike, which began on June 1, has turned into a demonstration of workers' power ahead of a leadership meeting this year that could see the ANC name a successor to Mbeki.
Union leaders had promised to shut South Africa down on Wednesday, but turnout was uneven.
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.
Workers in essential services, such as police, healthcare and emergency services, are barred from joining the strike, and some Cosatu unions, including the influential National Union of Mineworkers, did not join the boycott.
Many did, however, including those representing municipal workers. Mounds of refuse lay in city centres as rubbish collectors stayed off the job.
Charles Nqakula, the 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."
Pay rise demand
Public service unions are demanding a 10 per cent wage rise while the government of Mbeki counter offered with a 6.5 per cent increase. It has been suggested it may go as high as 7.25 per cent.
|Analysts say the strike is aimed |
at Thabo Mbeki, the president [AFP]
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."