The Atletico boss was sent to the stands in the early stages of an eventful game at Emirates Stadium on Thursday.
Having complained to officials following the red card shown to right-back Sime Vrsaljko in the 10th minute, Simeone was ordered to leave his technical area after demanding French referee Clement Turpin book Arsenal's Hector Bellerin.
UEFA has charged the former Argentina international with insulting a match official and improper conduct, with a disciplinary panel to judge the case on May 4, the day after the second leg in Madrid.
Simeone watched on from a higher vantage point than usual as Atletico secured a 1-1 draw thanks to Antoine Griezmann's late equaliser, giving them a crucial away goal ahead of the return fixture at the Wanda Metropolitano.
However, Simeone could be in the stands for the final of the tournament if he is handed a suspension, provided the LaLiga side make it that far.
UEFA also charged Atletico for their fans throwing objects during the game, while Arsenal could be punished for their supporters setting off fireworks.