Last month, Hungary had been ordered to play two home FIFA competition matches behind closed doors, one suspended for two years, following racist behaviour by supporters.
It came after September's home game against England in Budapest was marred by monkey chants aimed at Three Lions forwards Raheem Sterling and Jude Bellingham.
Hungary had been ordered by UEFA to play three home matches behind closed doors as a result of “discriminatory behaviour” by supporters at Euro 2020 but that did not include World Cup qualifiers, which fall under FIFA's remit.
With the Hungarian supporters under further scrutiny at Wembley, clashes broke out in the away section, with police appearing to use batons in an attempt to control the crowd.
The Metropolitan police tonight confirmed: "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."
A flare was also let off following Roland Sallai's penalty which put Hungary in the lead before John Stones equalised for England.
England were fined previously after their fans let off a flare during the Euro 2020 semi-final victory over Denmark.