The bodies of a female tourist and a local male guide were recovered after emergency services also abseiled down and rescued a second female tourist on Tuesday morning, said reports.
The accident happened on one of the country's major tourist attractions overlooking Cape Town.
The three hikers were using ropes when they fell and two of the climbers died after hitting the ground, the African News Agency has said.
It said South African National Parks spokeswoman Merle Collins confirmed they had been abseiling down the side of the mountain.
They had apparently been at an area known as "Arrow Final".
During the rescue operation, around 500 tourists were left stranded at the top of the mountain for hours before they were moved to the bottom in cable cars.
In a statement, Table Mountain Cableway, which operates the cable car service, said: "Our hearts go out to the families and friends of the two climbers who lost their lives.
"The hikers were spotted on the cliff's edge by Cableway staff at 5.15pm.
"After metro rescue conducted an assessment of the situation, we suspended operations at 6.15pm and assisted getting paramedics to the scene. Suspending operations also helped to limit the number of visitors at the top station.
"Due to the location of the climbers it was a very difficult and dangerous operation for mountain rescue.
"We are enormously grateful for the work of mountain rescue who risked their lives in this operation.
"We also thank them for assistance in providing transport to our visitors who did not have their own transport and required lifts home."