The game between the little-fancied Group B sides in the far-flung city was always going to be a tough sell.
Three thousand tickets were unsold to the clash in Nelson Mandela Bay stadium on the morning of the game.
But the empty seats in Nelson Mandela Bay stadium, one of five new stadiums built for the World Cup, far outnumbered the number of unsold tickets.
Just 31 500 out of 42 486 seater stadium were on hand to see South Korea win the game 2-0.
"It looks as if a number of people did not show up to the stadium. Obviously we've been investigating this," said Fifa spokesperson Nicholas Maingot at a press conference in Johannesburg.
For a few hard-sell games Fifa had made "some group sales of tickets to some large organisations", he said.
But the transportation to the game laid on for these groups "has not worked 100% yesterday obviously," he said, adding "We are making sure this is not the case for other games."
Apart from Port Elizabeth, Fifa has struggled to fill some games in Polokwane and the north-eastern city of Nelspruit -- the three most remote of the 10 World Cup host cities