The Group D game against the Germans on September 13th ended in a 1-0 win for Frankfurt but riot police had to intervene after fans launched fireworks and flares at each other.
Frankfurt also condemned one supporter who was caught making a gesture resembling a Nazi salute.
The UEFA Appeals Body also decided that Marseille must close the Virage Nord part of the Stade Velodrome for their subsequent home match in Europe's elite club competition against Tottenham Hotspur on November 1st.
UEFA ordered the partial ground closure "for lighting of fireworks, throwing of objects, use of laser pointers, crowd disturbances and blocking of public passageways".
Frankfurt must pay 45,000 euros in fines and have been handed a partial stadium ban, suspended for one year, for their next UEFA competition home game.
They have also been banned from selling tickets to their away supporters for their next UEFA competition match, also suspended for one year.
