The fans are also accused of having thrown objects during the match, while UEFA will investigate allegations of "improper conduct" from the supporters.
"Disciplinary proceedings have been opened against AS Saint-Etienne due to the behaviour of their supporters during their UEFA Europa League Round of 32 match against Manchester United FC on 16 February 2017 at Old Trafford," read a statement from UEFA.
"The following proceedings have been opened against AS Saint-Etienne for the following infringements: Setting off of firework - Art. 16 (2) of the UEFA Disciplinary Regulations (DR); Throwing of objects - Art. 16 (2) DR; Improper conduct of supporters - Art. 16 (2) DR."
The case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on March 23.