Yekaterinburg Arena (Gallo Images)
There were rows of empty orange seats at the freshly rebuilt arena in the industrial city, situated in the Ural Mountains, in a match that Uruguay won 1-0 thanks to an 89th minute winner.
The two soaring temporary seating sections at either end of the pitch appeared to be almost completely full, with one dominated by Egyptian fans and the other by the Uruguayans.
The seats are technically only supposed to be sold to Russian nationals.
FIFA said nearly all the available tickets had been sold and it was investigating why there were so many no-shows.
"We can confirm that 32 278 tickets have been allocated for the match between Egypt and Uruguay in Yekaterinburg. The Soccer World Cup stadium capacity is 33 061," a spokesperson for the football's world governing body told AFP.
"The fact that the actual attendance doesn't reflect the amount of allocated tickets can be due to different factors, which FIFA is currently investigating."
FIFA has allocated about 2.5 million tickets to the month-long showpiece, with Russian organisers saying that nearly all the tickets have already been sold.
Russians accounted for 46 percent of ticket sales, with the United States buying nearly 90 000.