In a statement, European football’s governing body said Spurs had been charged for “field invasion by supporters”.
The fan ran onto the field late in Spurs’ 1-0 victory on Tuesday and was confronted by Man City left-back Fabian Delph before being removed by stewards.
It was only the second match to be played at Tottenham’s new stadium, with Son Heung-min scoring the winning goal.
Ajax were also charged for throwing of objects, crowd disturbances and blocked stairways during their 1-1 draw with Juventus on Wednesday.
Download our app and read this and other great stories on the move. Available for Android and iOS.