The governing body's intervention comes after independent anti-racism group FARE tweeted reports of a neo-Nazi banner in the stands of die Mannschaft's final group game
The Football Against Racism in Europe (FARE) group had claimed that fans held up the sign during the match, which took place three days ago, on June 17.
"The DFB is charged with the setting-off of fireworks and the improper conduct of supporters (display of inappropriate banners and symbols, and inappropriate chanting)," the European footballing governing body said in a statement on Tuesday.
FARE, who have been working with Uefa in order to identify any race related problems at the competition, first reported the alleged incident via their Twitter account.
They tweeted on Tuesday: "FARE can confirm that one of our observers reported a neo-nazi banner in the German section at match versus Denmark game in Lviv on Sunday."
The charge comes after the DFB was already handed a €10,000 fine due to German supporters throwing, what were reported to be, rolled up pieces of paper at Portugal's players on June 9 in Lviv.
Uefa has dished out a number of fines to other nation's governing bodies so far in the tournament, with the Croatian Football Federation charged €80,000 for alleged racial abuse of Mario Balotelli from their fans and €25,000 for supporters littering the pitch with fireworks on another occasion, while Denmark's Nicklas Bendtner fined €100,000 for flashing a sponsor's name on his underwear after scoring.
Uefa will launch an inquest into the latest events on Saturday.