Islamophobic chanting was directed at Boro player Mido by a small section of Newcastle United supporters during the game.
A Middlesbrough FC spokesman said: "Middlesbrough FC has a very strong anti-racism stance.
"The club adopts a zero tolerance attitude towards racism and, working with the police, we will not hesitate to ban supporters identified as directing racial abuse against players or other fans, as we have in the past.
"Middlesbrough Police have confirmed that two individuals were arrested at the game for racial chanting and have been given a court date."
The males, aged 49 and 23, both from the Silver Lonnen area of Newcastle, will appear at Teesside Magistrates Court on Tuesday December 9 charged with racial chanting.