VIDEO: World Cup ticket delays
FIFA said 23 of the 64 games were sold out after tickets went on sale at ticket centres and banks across South Africa.
Match, the company employed by FIFA to run the ticket process, apologised for the glitches which led police to be called to centres in Johannesburg, Cape Town and Pretoria to calm frustrated fans.
Match chief executive Jaime Byrom said they "identified the challenges" and thanked fans for their patience.
About 500 000 seats were made available to local fans, the first time 2010 tickets could be bought for cash.
Earlier, police were called to the World Cup ticket center in Cape Town as FIFA's attempt to boost sluggish ticket sales made fans angry at the delays caused by technical difficulties.
A crowd gathered at the entrance to the center and chanted and yelled at organizers. Police were called to keep them calm.
After 3 hours, only 32 people out of a crowd of about 1 000 managed to buy tickets.
"No one's informed us what's going on. No one's directing the public outside. A primary school sports event could be better organised than this," said Theo Spangenberg, who had been waiting for 16 hours and still hadn't made it inside the newly opened facility. "For a World Cup, an international event of this nature, it's a really, really bad show."
The carnival atmosphere at the start of the day, as fans across the country were given a first chance to buy some of the 500 000 tickets still available, quickly disappeared in Cape Town. About 300 tickets for the final were to be sold on a first-come first-served basis.
Fans inside the ticketing centre slept on the floor as they waited to be served.
A representative from Match said she could not guarantee that every person would be helped on Thursday.
"I can understand there's a lot of frustrated people outside, and we have experienced some teething problems, since it is our first day," Christa Venter said. "The IT guys are well aware of the problem. Obviously it is a timely process, since we are experiencing quite high volumes at this stage countrywide."
Earlier in Cape Town, a 64-year-old man died of an apparent heart attack, but it was not related to the problems at the ticket office.
Local media also reported crowd scuffles at the ticket office in Pretoria.
The ticket centres opened across the country at 09:00 (SA time) for the last phase of sales. Thousands of fans lined up outside the Maponya shopping mall in Soweto - near where the opening game and the final will be held at Soccer City.
FIFA ticket centre manager Richard Lalla said the final tickets would last "a few minutes," but that was enough time for Marlin Fisher, a 32-year-old trainee church minister, who spent more than R10 000 rands ($1 370) on six tickets, including two for football's biggest game.
Fisher was first through the doors after queuing overnight and said it was "an incredible feeling" to have tickets.
"There are no words (to describe it). I've spent a couple of rands but it's all worth it," he said while holding his tickets up for photographers and TV cameras. "The Internet and applying was a bit frustrating but to be able to buy World Cup final tickets over the counter, that was amazing."
Fisher is one of many South Africans to be frustrated by FIFA's initial online process, which did not work for local supporters who are not used to buying tickets for football games on the Internet. Many are on low incomes and have no access to the Internet and no credit cards.
"I didn't even bother to go onto the Internet to buy because it was a waste of time to me," Nodoimpela Dlamini said as he waited patiently outside Maponya Mall. "Most of my colleagues who had applied through the Internet had been refused and actually couldn't get tickets."
FIFA and local organisers are under pressure to sell the remaining 450 000 match tickets for the monthlong tournament, which begins on June 11, to avoid a PR disaster of empty stadiums.
"I think the original process had to be put in place so that everyone across the country and across the world could have a fair chance to get their hands on some tickets," Lalla said. "Now that it is over the counter, I think our South African market is excited because this is what we are used to, this is our culture. It's more for our market now and people will do really well with the tickets that are left."
In Sandton, an upper class area in Johannesburg, the city's second ticket centre was also hit by technical problems. Ticket machines had "out of order" signs on them and police were called to watch over the disgruntled fans.