The reversal comes after SATAWU had called a three-year wage hike agreed on by Transnet and the majority United National Transport Union (UNTU) a "betrayal."
"We have called off the strike and our members are going back to work tomorrow," SATAWU spokesperson Amanda Tshemese told Reuters on Wednesday.
The unions walked out on October 6 demanding wage increases linked to South Africa's year-on-year inflation rate, which was 7.5% in September.
But UNTU and Transnet settled on a 6% increase for this year, followed by another 5.5% in 2023 and 6% the year after.
SATAWU had pushed for a bigger hike, first demanded at 8%.
Fresh produce exporters who, along with miners, were among the most affected by the strike, said port operations had started to improve on Wednesday.
The labor action had a notable impact on several important South African business sectors. The nation's Minerals Council said mining companies were losing 815 million rand ($44.62 million) per day in export revenue due to the strike, as major mineral export harbors were operating at between 12% and 30% of their daily averages.
