Many irate fans had tweeted about their frustrating ticket buying experiences to the singer.
One fans, Nabeela Noorani @NabzNoorani, told Lady Gaga that she had waited in the online queue for hours before the system crashed.
"Waited 3.5 hours!! And then it crashed!!!!!! There bettr still b tickets," she tweeted.
"I waited for 8 hours in a queue to see you Mother Mons†er in Johannesburg. Loooooove you!!" wrote @RiaanSmal.
@AyandaNdlovu also told the Pokerface singer that he had struggled to obtain his tickets. "@ladygaga we love you! Waited ages just to get a ticket!" he said.
The Born This Way singer tweeted to her 26 million followers:
Just woke up to emails saying South African monsters crashed the online ticket servers due to high demand for TheBTWBall! I cant believe it!— Lady Gaga (@ladygaga) June 19, 2012
Late on Tuesday night event organisers, Big Concerts released a statement on their Facebook page:
"Due to demand, the ticketing system experienced a nationwide outage today and web sales have been sporadic as a result.
"To rectify the situation and to ensure that all fans have the best possible access to tickets, online ticket sales have been discontinued for the evening," they said.
Online ticket sales were re-opened at 09:00 on Wednesday and the Shoprite Group announced they would be selling tickets over the counter for both the Cape Town and Johannesburg shows at their Money Market stores a day earlier than anticipated.
Shoprite Group Chief Executive Officer Whitey Basson said they were "unhappy" with Computicket's decision to relent to the insistence of the tour promoters to reserve ticket sales for internet users for the first 48 hours.
Lady Gaga is set to perform at the FNB Stadium in Johannesburg on 30 November and at the Cape Town Stadium on 3 December.