The Scottish Champions received a charge for the incident at the San Siro just two days after being fined for an identical offence in their previous Europa League trip against Dynamo Zagreb.
Ronny Deila???s side were also hit with another charge for their team’s behaviour in the 1-0 second-leg defeat by Inter Milan on Thursday night.
Celtic will contest the “improper conduct” charge which was sparked by their card count in the away leg.
However, their biggest concern is to stamp out the trend in lighting flares at away games after being hit with a seventh UEFA charge for fan behaviour in little over three years.
Celtic had appealed for fans to behave at the San Siro after being fined ??7,300 on Wednesday after a supporter let off a flare during their group match against Dinamo Zagreb in Croatia.
But pyrotechnics were evident in the visiting section in Milan and both clubs have received the same charge.
A Celtic statement read: “Over 3,000 fans travelled to Milan and once again supported the club brilliantly. Everyone at Celtic thanks these fans sincerely for the magnificent support they gave the team on another European occasion.
“It is important to note that Inter Milan and the local Italian authorities have also applauded our fans for their excellent conduct and positive support.
“Unfortunately, one or two individuals have again damaged the club they claim to support, resulting in a further UEFA charge for the use of flares.
“Today we have been inundated with support from Celtic fans who want an end to this activity and, like the club, do not want those responsible associated with Celtic in any way.
“We would urge anyone with information on who these people are to get in touch with the club so that we can deal with this matter and get back to celebrating all that is great about our club.”
Celtic’s players are also in the dock after Virgil van Dijk was sent off following two bookable offences in the first half of their defeat, which saw them lose 4-3 on aggregate, and a further five players were booked.
A club spokesperson said: “UEFA rules state that they are able to open disciplinary proceedings against any club which receives five or more bookings. Celtic can confirm that this is a charge which the club will be contesting.”
Manager Ronny Deila criticised referee Ivan Kruzliak for his decision to send off the Dutch defender while skipper Scott Brown felt the Slovakian official had been too harsh throughout.
Brown, who was not booked, said: “Football is a man’s game, there’s always going to be tackles that are a wee bit late due to the pace of the game. These things happen but every single tackle shouldn’t be a yellow card.”
UEFA’s control, ethics and disciplinary body will consider the charges on March 19.