The charge that the Portugese club will face - according to UEFA - is for public disturbance which saw fans throw flares and objects towards the players. While Atletico are being investigated for blocked stairwells.
Both cases will be analyzed by UEFA's Committee for Control, Ethics and Discipline on the 15th of October.
In the 36th minute of the first half, Benfica fans from the upper two tiers of the north stand started launching flairs towards the fans who were directly below them the moment that Nico Gaitán scored to level the match at 1-1.
Some of them landed on several rojiblanco fans and it meant that the game had to be stopped while they were put out
After the Portuguese side went ahead in the 51 minute, another flare was but it was sent flying towards the Lisbon team, where seats were also broken.
Atletico Madrid said on Thursday it had taken "the usual safety and prevention measures" and that control access "numerous flares and other objects seized" to followers of the Portuguese club, whose president, Luis Filipe Vieira apologized for what happened.
For similar incidents Control Committee, Ethics and Disciplinary UEFA has sanctioned with fines above both clubs acting as locals and visitors and sometimes with partial closures of its stands if other infringements are added