UEFA said in a statement that St Etienne, who face a fine, were charged with setting off fireworks, throwing objects and the improper conduct of supporters at Old Trafford on Thursday.
It said its control, ethics and disciplinary body would met to deal with the case on March 23.
The Ligue 1 side, whose fans lit up the away end with smoky green and red flares, lost the match 3-0 with Zlatan Ibrahimovic scoring a hat-trick.
Some Manchester fans questioned afterwards how the visitors had managed to get so many flares through supposedly tight security at the stadium.
"There is heightened security at the moment at United. If you turn up you get searched at the door, you walk up to the turnstile, you get searched," United supporter Keith Bradley told the Manchester Evening News.
"But then you see in the ground at least 20 to 30 flares going off last night."
(Reporting by Alan Baldwin; Editing by Alison Williams)
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