Germany fans displayed "inappropriate banners and symbols" and were responsible for "inappropriate chanting," UEFA said in a statement. Fans also set off fireworks at Sunday's match in Lviv, Ukraine.
German fans have now provoked UEFA charges after all three of the team's matches at Euro 2012.
Portugal players were pelted with crumpled paper balls during the teams' first match in Lviv. UEFA fined the German association €10,000 ($12,550).
After Germany played the Netherlands in Kharkiv, UEFA opened a case for fans setting off fireworks and throwing more paper balls. UEFA has not yet published a ruling.
UEFA said its disciplinary panel will deal with the latest case on Saturday.
Germany beat Denmark 2-1 to advance to a quarterfinal match against Greece on Friday, in Gdansk, Poland.