The Greek side has been charged with use of laser beams against players by their supporters, throwing of missiles and "insufficient organisation (lack of body search)," during their 3-1 win, UEFA said.
The French visitors were charged with crowd disturbances and "setting off and throwing of fireworks".
Media reports said around 100 Montpellier fans clashed with riot police before the Group B game. The hearing will take place on Nov. 22.
UEFA said Olympiakos would also face action over the "improper conduct of the team", a charge which is brought automatically against any side which receives five or more yellow cards in a game.
Greek football has been beset by crowd violence.
In a recent case, PAOK Salonica were ordered to play their next three European matches behind closed doors following a riot at a Europa League qualifier at home to Rapid Vienna in August.
PAOK will also have to pay a 150,000 euro ($193,458) fine and face automatic expulsion from European competition if there is a repeat incident within the next three years.
Fans hurled a variety of firecrackers and other missiles at each other, and at one point dozens of masked fans ran onto the pitch.
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