The United National Transport Union (UNTU), the majority union, has agreed to a six percent wage hike offer, down from their demand of almost eight percent.
Workers at Transnet, which operates the freight rail network and ports in Africa's most advanced economy, walked out on October 6 demanding a better deal.
The strike cost mining firms 815 million rand ($45 million) in exports a day, according to the Minerals Council South Africa, an industry group.
Major mineral export harbors ran at only 12 to 30 percent of their daily average, the group said last week.
Transnet vowed to immediately start implementing a recovery plan following the strike action, which stranded mineral and fresh fruit exports.
"The company's priority in the immediate is clearing any backlogs across the port and rail system," it said.
Worked resumed on Monday evening.