Fifa general secretary Jerome Valcke told BBC Sport the game’s governing body signed off the 25% increase at an executive committee meeting in March.
He said the extra money was required to help the South Africans ensure team training camps were ready.
South Africa’s organisational budget has now swelled from £282m to £349m.
But Valcke insisted Fifa’s £2.1bn income from the tournament would more than cover the overall increase in its budget, which includes the South African allocation, from £733m to £800m.
England officials expressed deep concern about the team’s World Cup base, particularly the state of the training pitches, when they visited the Royal Bafokeng Sports Campus in December.
But England coach Fabio Capello is now understood to be happy that it is ready for his team’s arrival next month.
“We know we had to add some money for the team base camps where some teams were unhappy about the level of the services or the level of the pitches,” said Valcke.
“That’s a cost Fifa took over to ensure that things were delivered on time.”
With exactly one month to go to the start of the World Cup on 11 June, the Frenchman said he was confident the South African organising committee would not require any further funding from Fifa.
He also said he was sure South Africa was ready to stage the tournament and added he was confident the event would leave a lasting legacy on the country and the African continent.
“A lot of people are trying to say the World Cup will be like the Rugby World Cup in ’95 and the first election in ’94,” he said.
England’s World Cup base is the Royal Bafokeng Sports Campus
“I hope the final result of this World Cup will be that the two communities in South Africa will be a different country by the end.”
Valcke defended the vast sums of money made from the sale of television and sponsorship rights relating to the World Cup, insisting that the governing body made no profit.
Any surplus, he explained, was re-invested in development football programmes or national associations around the world.
“The World Cup is the most beautiful football event, played every four years with the best teams of the World,” said Valcke.
“It’s a unique event, and that’s why there is such interest. Yes, it’s a lot of money but we are not sitting on profit.”
In addition to the £800m spent by Fifa, South Africa has paid out a staggering £3.5bn on building and redeveloping 10 stadiums, creating a new transport infrastructure and ensuring security is up to scratch.
Gillian Saunders, who has conducted extensive research on the finances of the 2010 World Cup for accountants Grant Thornton, said expenditure on the event represented just 1.72% of South Africa’s gross domestic product (GDP).
She said the country could afford the costs and that the tournament had helped to protect its economy from the fall-out from the global economic downturn.