A number of England supporters joined in the singing of a song suggesting the brothers should be burned on a bonfire.
The Manchester United defender was vilified by fans after withdrawing from the England squad to play the game because it did not fit in with his "intricate" and "pre-planned" training programme, although he then travelled to Qatar to commentate on England's 8-0 victory.
Rio Ferdinand tweeted: "You expect+accept banter from fans on the terraces as its part of what makes the game great,but racism is not banter,& from ya own fans. WOW.
"Always a small minority who ruin it for others.
"Let's not jump to conclusions + assume though as it might just have been banter. We'll see after the investigation."