Police clashed with supporters in the away end as they entered the stand to arrest an individual for over an alleged incident of racist abuse directed as a steward, with television pictures showing officers using batons in attempt to hold off the crowd, before themselves being forced back into a stairwell.
The Metropolitan Police described what happened as “minor disorder”.
Elsewhere in the same qualifying group, the match between Albania and Poland game in Tirana was temporarily suspended. Bottles were thrown on to the pitch after Karol Swiderski scored for Poland in the 77th minute.
Football’s world governing body said in a statement: “Following an analysis of the match reports, FIFA has opened disciplinary proceedings in relation to yesterday’s England v Hungary and Albania v Poland FIFA World Cup qualifier matches.
“Once again, FIFA strongly condemns the incidents at both matches and would like to state that its position remains firm and resolute in rejecting any form of violence as well as any form of discrimination or abuse. FIFA has a very clear zero-tolerance stance against such abhorrent behaviour in football.”
Hungary were ordered to play two matches behind closed doors, one suspended for two years, over the racist behaviour of their fans during the qualifier against England in Budapest last month.
Raheem Sterling and Jude Bellingham were targeted with monkey chants during the match on September 2, which England won 4-0.
In July, European football’s governing body UEFA imposed a two-match stadium ban on the Hungarian federation following an investigation into the behaviour of their supporters during Euro 2020 matches in Budapest and Munich.
Additional reporting by PA.