UEFA announced on Sunday afternoon they had begun disciplinary proceedings against the German Football Association over the behavior of their fans during the country's 1-0 Group B win in Lviv.
Supporters threw screwed up paper at Portugal's players during some corner kicks at the Arena Lviv and let off a smoke bomb in the stands.
They were repeatedly warned over the public address system that such acts could result in their ejection, sanctions for their team, and even abandonment of the match.
UEFA said in a statement: "UEFA confirms that it has opened two disciplinary proceedings following Saturday's UEFA Euro 2012 Group B match between Germany and Portugal in Lviv.
"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 kick-off to the second half.
"The UEFA Control and Disciplinary Body will deal with the case on Thursday 14 June."
UEFA charged the Russian Football Union on Saturday over the behavior of their fans during Russia's 4-1 win over Czech Republic on Friday, which included alleged racist chanting and an attack on several stewards