England supporters without tickets charged the barriers outside Wembley ahead of the game and found their way inside the stadium, while a fan also invaded the pitch during the second half.
The FA have also been charged for supporters throwing objects inside the stadium and for disturbance after fans booed during the Italian national anthem.
UEFA have not charged the FA for those who illegally entered the stadium but have instead appointed an investigator to look into the events which saw hundreds of ticketless fans break through the security cordon and into the stadium.
A statement from the European governing body read: “Separately, and in accordance with Article 31(4) DR, a UEFA Ethics and Disciplinary Inspector has been appointed to conduct a disciplinary investigation into events involving supporters which occurred inside and around the stadium.”
The FA, who were also charged by UEFA following England’s semi-final against Denmark, have confirmed they will conduct a full review into the circumstances around Sunday’s final while chief executive Mark Bullingham branded those who had broken in without tickets “drunken yobs”.
Bullingham told the BBC: “There were a large number of drunken yobs trying to force their way in, we run a stadium not a fortress.
“I have to apologise to any fans whose experience was affected and any of the team who had to cope with this.”