Dozens of red and green flares were set off in the away end of Old Trafford shortly before kick-off, causing a significant amount of smoke to billow across the pitch.
UEFA has announced that they will investigate alleged breached of two other crowd offences, with the organisation's Control, Ethics and Disciplinary Board to convene on the issue on March 23.
"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 February 16, 2017 at Old Trafford," a statement confirmed.
"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."
United triumphed 3-0 to secure a substantial aggregate lead, thanks to Zlatan Ibrahimovic's first hat-trick for the club.