It is the second time this month that the club have been charged by European soccer's governing body.
During Spartak's 1-1 draw in their group opener at Slovenian champions NK Maribor on Sept 14 a flare fired from the visiting supporters' stand almost hit German referee Deniz Aytekin.
The club were fined 60,000 euros (52,580.55 pounds)and banned from selling tickets to supporters for their next away match in Europe, at Sevilla on Nov. 1.
UEFA's Control, Ethics and Disciplinary Body will deal with the latest case on Oct. 19.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Ken Ferris)
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