The Spanish manager was charged for communicating with the team's technical staff in the second half according to Article 69(1) of UEFA's Disciplinary Regulations.
UEFA also charged Liverpool after their fans set off fireworks and threw objects inside the Etihad Stadium.
The case will be heard by UEFA's Control, Ethics and Disciplinary Body on May 31.
Liverpool completed a 5-1 aggregate victory to reach the semi-finals of the Champions League.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Toby Davis)
