The game, which PSG won 6-1 at the Parc des Princes, is also being probed by French investigators over suspicions of match-fixing by the Serbian champions, when a senior official of the club allegedly bet millions of euros on the team to lose by five goals.
The Ligue 1 leaders have been charged over "setting off fireworks" and "crowd disturbances", and were also fined 20,000 euros ($22,960) for a delayed kick-off.
As PSG had already had one stand closed due to flares being let off during last season's last-16 exit to Real Madrid, they could be handed a heavier penalty if found guilty this time.
PSG coach Thomas Tuchel was also given a warning by UEFA over the late kick-off.
In addition to the incidents inside the Parc des Princes, clashes erupted between fans and police after the game outside the stadium.