Three pitch invasions were orchestrated as an internet prank and caused the match to be suspended for around 10 minutes just before half-time.
A video posted on YouTube shows three men planned the disturbances.
European football's governing body will hear the charge on 11 December.
Spurs had earlier apologised in a statement for the "totally unacceptable behaviour".
The pitch invaders were all arrested after they disrupted the game have been revealed revealed as YouTube stars making films that aim to 'offend and harass the general public'.
Gomes Garcia, Nathan Brown and Dan Jarvis are the founders of TrollStation, a controversial prank group.
Two days ago one of the group's founders tweeted a picture holding a picture of Nathan Brown holding a YouTube award
One member also pretended to take cocaine in public places and another confronted comedian Russell Brand at a 'People Before Profit' rally he organised.
Police have also been called to speak to them on a number of occasions.
Before their latest prank at Spurs, Garcia, Brown and Jarvis filmed themselves boasting about how they would disrupt the match and also chanted 'Yid Army' - a controversial phrase linked to Spurs' Jewish support which some consider anti-Semitic.
The trio ran on to the pitch during the first-half of the Europa League match, attempting to take selfies with the Tottenham players and evading stewards who tried to catch them.
After the third pitch invasion, referee Yevgen Aranovsky led the players into the tunnel for several minutes on safety grounds.
The men were all wearing T-shirts bearing the name of a headphone manufacturer - BassBuds - who issued a statement via Facebook condemning their actions, adding: 'We are appalled that the game was interrupted in this manner. We do not condone the interruption of any sporting fixture in this way.'
Despite this, Spurs severed links with the company after the stunt and could well take legal action if they are found to have links to it.