Hundreds of football fans missed the match between the two European football giants on Wednesday after chaos at the airport in the coastal city delayed their landing or forced planes to turn back.
Airports Company South Africa (ACSA) said bad weather, larger than expected traffic and VIP planes which refused to move from the airport - as had been agreed in advance - caused the chaos at the new Durban King Shaka International airport.
Some 600 passengers missed the match after six planes were forced to either return to Johannesburg or Cape Town, or divert to other airports.
ACSA Chief Executive Monhla Hlahla officially apologised for the airport disarray, a rare blemish on the so far successful hosting of the World Cup, held on the continent for the first time, which has gone without any major glitches.
"We have decided that we will put aside a small amount of money to the tune of 400,000 rand ($52,850) to compensate (passengers)," she told Talk Radio 702.
This might not be enough to compensate many fans. Some said they spent up to 30,000 rand on flights and match tickets. Stranded passengers, who spent thousands of rand on flight and match tickets, were outraged by the mismanagement that led to the problems.
A German fan was due to appear on court on Friday for allegedly assaulting a cabin crew member after realising that he would miss the much anticipated match after his plane was diverted to Port Elizabeth, officials said.
"He behaved in a violent manner towards a crew member and will appear in court today," said Mthunzi Mhaga, spokesman for the National Prosecuting Authority.
ACSA said it would ensure there would be no repeat of the problems during the World Cup final at Soccer City in Johannesburg on Sunday when Netherlands face Spain.
If aircrafts refuse to move, the company threatened to tow them out of the way to clear the landing and airport space.
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