Roads in the city had been jammed for much of the day on Monday meant trips to the airport were taking twice as long as normal.
The new Gautrain, which runs to the ritzy Sandton district where many fans are staying, could be a godsend.
It ferried its first passengers from Sandton to the international airport in 15 minutes early on Tuesday at a speed of 160 kph, compared with normal road journeys of 40 to 90 minutes depending on traffic.
A single ticket to the airport costs 100 rand ($13.50), prompting criticism that it will be too expensive for working class South Africans.
The train will eventually link Johannesburg and the sprawling township of Soweto to the capital Pretoria, but constructors rushed to finish the Sandton leg in time for the World Cup.
Johannesburg and other World Cup venues have been disrupted for years by massive urban infrastructure projects including the 25 billion rand ($3.38 billion) Gautrain line being built under the city, which has involved blasting through rock, and extensive new road building.
City authorities say the remaining construction work will be suspended during the tournament starting on Friday to ease traffic but FIFA has expressed concerns that jams will prevent fans filling the majestic Soccer City stadium near Soweto in time for Friday's opening ceremony.
They appealed to South Africans, notorious for arriving late at matches, to get there early.
