Gaga was scheduled to arrive at Lanseria Airport around 17:50 but was delayed as her private jet had to refuel at Cape Town International Airport, reports said.
5FM reported that fans were left disappointed after her security "opted out of a grand entrance due to concerns about the Lanseria crowd".
She is scheduled to perform at the FNB Stadium Soccer City complex on Friday 30 November and at the Cape Town Stadium on Monday 3 December.
Big Concerts recently announced that extra tickets for her concert in Johannesburg had been released.
There was, however, opposition to her appearances in the country as the South African Council of Churches had planned planned to prevent the performances, and marched to the department of Arts and Culture in Pretoria.
The church group had raised concerns, stating that they were in fact worried about the "destructive impact" Lady Gaga could have on South Africa's youth.
Reverend Mxolisi Sonti, secretary of the youth forum, told Beeld they were afraid of the extent of Satanism in South Africa at this time, and that Gaga's visit could lead to an exponential growth of Satanism.
He also claimed that if the government could stop the Dalai Lama from coming to South Africa, then they could stop Lady Gaga as well.
Culled from News24