The industrial action threatens to paralyse operations at Transnet, disrupting the rail movement of key commodities, supply of coal to power stations, vehicles and fuel supply.
Transnet operates the country's ports, freight railway networks, and fuel pipelines.
The South African Transport and Allied Workers Union (Satawu) said on Tuesday it expected the movement of goods and fuel by Transnet to be "totally shut down by this evening".
Utatu's decision on Tuesday to join in the strike means that it was now embarking on a nation-wide industrial action that was started on Monday by Satawu.
Utatu, which did not embarked on a strike on Monday, represents 45% of workers.
The two unions accounting for around 84% of Transnet's workforce will now partake in the strike and about 50 000 workers are involved.
On Monday, the strike spiralled out of control sparking violence and intimidation. About 13 protesters were arrested in Durban on charges of public violence, assault and intimidation.
After Transnet revised its original 8% wage offer to 11% on Friday, Utatu leaders recommended it to its members as "definitely good".
But Utatu said on Tuesday its members had stuck to their original demand of 15% and will formally embark on the strike from Wednesday.
Transnet warned on Thursday that the 15% wage hike would force the company to either increase tariffs, or reduce its capital expenditure, or cut jobs.
It also said on Thursday that the unions' 15% wage demand would add about one billion rand to its operating costs.
Satawu said this should be a signal to Transnet to start thinking "seriously" about coming to the negotiating table with a "seriously" adjusted offer, unlike the so-called 11% offer delivered to the unions on Friday.
Transnet said on Monday it was strengthening its contingency plans and had managed to minimise the impact of the strike on critical flows.
Public Enterprises Minister Barbara Hogan said on Tuesday she had "full confidence" in the parties involved in the wage negotiations.
The minister said she was "hopeful" that a solution that satisfied all parties would be found.
Commenting on the strike, Ross Bruton, energy analyst at Frost & Sullivan, warned this week that a disruption in the fuel supply would have a substantial effect on the availability of products to the market.
On Thursday, the South African Chamber of Commerce and Industry said the strike could halt the delivery of coal to power stations with consequent power interruptions.
Recently, the National Association of Automobile Manufacturers of SA said the industrial action would be "extremely damaging" to the automotive.
