The City manager faces a first charge having been sent to the stands for protesting to referee Antonio Mateu Lahoz after Leroy Sane had a goal incorrectly disallowed during the quarter-final second leg at the Etihad Stadium.
Guardiola also faces a second charge of improper conduct from the European governing body for communicating with the bench after he had been sent to the stands.
UEFA has also charged Liverpool over the behavior of their fans during the game, for letting off fireworks and throwing objects.
The game’s major flashpoint came when City, leading 1-0, was denied a second goal late in the first half when Sane was ruled offside despite the ball having come to him off Liverpool’s James Milner.
It prompted an angry reaction from City that continued after the half-time whistle, with Guardiola entering the field. He was ordered to watch the remainder of the game from the stands.
Under Article 69 of UEFA regulations, Guardiola would then have been forbidden from communicating with the technical area but the governing body believes there may have been a breach.
Liverpool won the game 2-1 to complete a 5-1 aggregate success.