Football's governing body put 90,000 new tickets on the market, including seats at the previously sold-out final and semi-finals, causing a new rush by South Africans.
Some people had been queuing for more than 24 hours to get tickets but when the system opened it immediately collapsed, as it did last month when over-the-counter sales first began in South Africa.
Overflowing queues caused delays on one commuter route in Johannesburg.
FIFA secretary general Jerome Valcke issued an apology over the problems as police were called to control the crowds in Johannesburg. At one point, they closed the doors to a ticketing office in the city's Sandton district.
"It's FIFA that does not have a system in place that is letting South African people look stupid because they must have anticipated this would happen," said one woman in the line, Amelia Rawllan.
"This is rubbish, complete rubbish. People are pushing in and there is no order," Bongwa Mthembu added.
The tickets were on sale at supermarkets and bank branches as well as special counters but all relied on FIFA's computer system. One man, Vanesh Reddy, had been waiting outside a ticketing office since Wednesday.
FIFA said in a statement that significant delays occurred in all sales outlets.
"I would like to sincerely apologise to all the fans that have been affected by the problems in the ticketing sales system," Valcke said.
The system came back on line later but there were still long delays and lines of angry fans.
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