UEFA's control, ethics and disciplinary body will now deal with the case when it meets on Novemeber 16.
Old Trafford seems to attract the use of pyrotechnics of late, with Basel last month given a €12,000 fine after their fans set off flares before their Champions League opener against United in September and French side Saint-Etienne slapped a €50,000 fine in March for the use of flares and for throwing projectiles during a Europe League last-32 game at the 'Theatre of Dreams'.
Despite Benfice bringing the flares, it was United who were left celebrating after the game, with Jose Mourinho's side now needing just one point to qualify for the Champions League knockout stages for the first time in four years.