Travelling supporters had already booed England players taking the knee and held up a flag objecting to the anti-racism gesture ahead of kick-off and were then tussling with police within the opening five minutes.
Metropolitan Police officers used batons to try and control the crowd but were forced to retreat to the concourse following the clashes.
In a statement, the Met said: “Shortly after the start of tonight’s match at Wembley, officers entered the stand to arrest a spectator for a racially aggravated public order offence following comments made towards a steward.
“As the officers made the arrest, minor disorder broke out involving other spectators. Order was quickly restored and there have been no further incidents at this stage.”
The Football Association said: “We are aware of an incident in the away section during tonight’s FIFA 2022 World Cup Qualifier at Wembley Stadium. We will be investigating and will report the incident to FIFA.”
It comes after a string of incidents involving the nation’s supporters during the European Championships and in games since. UEFA have ordered Hungary to play a game behind closed doors following racist abuse from supporters and homophobic banners in the stands during their Euro 2020 group stage matches.
England’s players were then subjected to racist abuse by supporters during their 4-0 win in Budapest last month. Supporters were allowed to attend that game as it was under the jurisdiction of FIFA.