England's 4-0 win at Puskas Arena in Budapest was overshadowed by the alleged behaviour of certain sections of the home crowd.
Raheem Sterling and Jude Bellingham were reportedly subjected to abuse and missiles, including a flare, were launched towards the Three Lions' players during the match.
England condemned the abuse as "completely unacceptable", while British prime minister Boris Johnson called on FIFA to take "strong action" against the perpetrators.
The world football governing body announced on Saturday (AEST) it will now look into the scenes.
"Following analysis of the match reports, FIFA has opened disciplinary proceedings concerning the incidents last night at the game Hungary-England," a statement read.
"Once again, FIFA would like to state that our position remains firm and resolute in rejecting any form of racism and violence as well as any other form of discrimination or abuse.
"We have a very clear zero tolerance stance against such abhorrent behaviours in football."
The Hungarian Football Federation (MLSZ) was fined €100,000 ($161,420) in July and ordered to play three games behind closed doors, the third of those suspended, because of incidents of racism and homophobia from fans during the European championship finals.
The MLSZ vowed to "severely punish" fans who disrupted the England clash by launching missiles and entering the pitch, but the governing body steered clear of addressing the alleged racism incidents.
After Friday's (AEST) latest incident, Bellingham has questioned whether enough is being done to eradicate racism from the sport.
Alongside a photo of himself smiling while warming up for the game in the Hungarian capital, Borussia Dortmund youngster Bellingham tweeted: "Thank you for all the messages of support from last night.
Thank you for all the messages of support from last night. Part of the game and always will be until proper punishments are put in place by those with the power. We can’t let hate win, keep smiling!😁❤️ pic.twitter.com/nP3zarQBQk— Jude Bellingham (@BellinghamJude) September 3, 2021
"Part of the game and always will be until proper punishments are put in place by those with the power. We can't let hate win, keep smiling."