"The protest turned violent with stone-throwing and damage to two vehicles, but no one was injured as far as we are aware," the power utility said in a statement on Wednesday.
"The situation is under control and calm has been restored on site."
Eskom was referring to a wildcat strike at its Medupi plant which turned violent; with two cars stoned and unconfirmed reports that they were set alight by protesters.
Between 500 and 1 000 striking workers began protest action at the massive-scale coal fuelled plant, which is still under construction.
Eskom said most Medupi workers had been sent off site, but the utility was working to get operations back to normal as soon as possible.
"The protest apparently related to dissatisfaction with one of the allowances which workers receive, which is currently the subject of negotiation."
Two weeks ago, Eskom said in a statement the new power station would probably begin contributing to the national grid only in the second half of next year because of construction problems. The previous target was December.
Public Enterprises Minister Malusi Gigaba insisted earlier this year that the December deadline would not change.
Twitter reports
Reports on Twitter said several people had been injured in violent confrontation between protesters and the police, but Eskom did not confirm this. "The protest turned violent with stone throwing and damage to two vehicles, but no one was injured as far as we are aware," it said.
Unions and management at Eskom are currently in a deadlock over wage negotiations. The public owned company has offered a wage increase of 5.6% to the workers, but unions have dismissed this as an "insult".
Dissatisfaction with the negotiation process has already led to small-scale protests at four key Eskom power stations, including Matimba, Duvha, Matla and Hendrina over the past two weeks.
Last Friday, leaders from major union representatives the National Union of Metalworkers of South Africa and the National Union of Mineworkers warned that unhappiness at other power stations would likely see further work stoppages.
Eskom approached the Labour Court last week in a bid to have any strike action by its employees recognised as unlawful, on the grounds that the company is a "designated service provider". It also asked the court to compel unions to issue a statement urging workers to remain at their posts.
But union leaders said they would do no such thing, and that workers were so angry that such an encouragement would not serve to quell them. – Additional reporting by Sapa