The upper tier section of around 200 seats was filled by tournament volunteers later in Friday's match, which ended 1-1.
FIFA said 84,490 people attended at Soccer City, a record for one of its matches in Africa.
"There was one block that looked empty and our people in ticketing are looking into it," FIFA spokesman Nicolas Maingot said Saturday.
All tickets were sold for Saturday's matches between England and the United States at the 45,000-seat Royal Bafokeng stadium in Rustenburg, and at 62,500-seat Ellis Park in Johannesburg. where Argentina faced Nigeria, FIFA said.
However, the 46,000-capacity Nelson Mandela Bay stadium in Port Elizabeth was only about two-thirds full for South Korea's 2-0 win over Greece. FIFA said only 3,000 tickets were still available early Saturday, but that many ticket holders simply didn't show up for the game.
The official attendance was 31,513 in Port Elizabeth.