The Chilean accused Swedish referee Jonas Eriksson of failing to be "impartial to both teams" in Manchester City's 2-0 loss to Barcelona and could now face a fine and ban.
City was reduced to 10 men when Martin Demichelis conceded a penalty for a foul on Lionel Messi - a decision that angered the Chilean manager when replays showed contact started outside of the box - and Barcelona went on to triumph 2-0 at the Etihad Stadium.
|MAN CITY LATEST
UEFA responded Thursday by announcing it would investigate Pellegrini's comments and has now formally charged the former Malaga boss.
"Following an investigation by the UEFA disciplinary inspector, UEFA has today opened disciplinary proceedings against Manuel Luis Pellegrini concerning the press interviews given to media after the above-mentioned match," a statement read. "The Manchester City FC head coach is charged for violation of the general principles of conduct (Art.11 of the 2013 UEFA Disciplinary Regulations).
"The case will be dealt with by the UEFA Control and Disciplinary Body on Friday 28 February."
Pellegrini is likely to face both a substantial touchline ban and fine.