UEFA charged Germany on Sunday after its fans threw crumpled paper balls at Portugal players during a European Championship match.
Portugal has also been charged for being late out for the second half on Saturday at Lviv, Ukraine. Both teams could face financial penalties.
''The German Football Association (DFB) is charged with the throwing of missiles by its supporters, while the Portuguese Football Federation (FPF) faces proceedings for a delayed kickoff to the second half,'' UEFA said in a statement.
UEFA said its disciplinary panel will deal with the cases Thursday.
Portugal players were pelted with dozens of grapefruit-sized paper balls during the first half of Germany's 1-0 victory. A stadium announcement warned Germany's fans that their team would be punished if they continued the barrage.
UEFA has now brought charges against three of the eight Euro 2012 nations which played on the first two days of the three-week tournament.
On Wednesday, UEFA will judge an improper conduct charge against Russia for its fans' behavior during and after a 4-1 win against the Czech Republic.
Russian fans were filmed attacking stadium stewards in Wroclaw on Friday. They also displayed a nationalist flag and threw fireworks on the pitch.
UEFA is also seeking further evidence to prove claims that Russian fans racially abused Czech defender Theodor Gebre Selassie, who told The Associated Press on Sunday that he noticed the insults aimed at him.
''It was nothing extreme. I've experienced much worse,'' the 25-year-old defender, whose father is Ethiopian, said.
Russia's football federation called on its supporters to show more respect at Euro 2012, and warned that UEFA could punish the team with a points deduction.
In a similar case to Portugal's, Manchester City was fined ?30,000 ($39,400) by UEFA this season for returning to the field late in a Europa League match against Sporting Lisbon.
