Long queues backed up for the train service which had 20,000 to 25,000 passengers, less than a week after the three billion dollar project was opened.
"We were just overwhelmed by the huge number of people coming to visit us. It did put a massive strain on the facilities, which took a little bit of time to recover," said Errol Braithwaite of the operator Bombela.
"The use of public transport during this time will significantly reduce congestion on the roads," he said, pointing to overhauled systems which include bus and train networks.
"Too many fans are driving in private vehicles and the use of public transport will assist a great deal."
The train was used by 1,000 commuters in the first hour on its opening day and is seen as a major move to free up Johannesburg's gridlocked roads.