The German Football Association (DFB) was docked 10,000 euros (£8,092) for "the throwing of missiles" by their supporters during the Group B match in Lviv.
German 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.
The Portuguese Football Association (FPF), meanwhile, was fined 5,000 euros (£4,046) for a delayed kick-off to the second half at the same game, a rule breach that got Manchester City a 30,000 euro fine in the Europa League this season.
UEFA said in a statement: "The German Football Association (DFB) has been fined 10,000 euros by the UEFA Control and Disciplinary Body for the throwing of missiles by its supporters at last Saturday's UEFA EURO 2012 Group B match between Germany and Portugal in Lviv.
"The Portuguese Football Association (FPF) has been fined 5,000 euros for a delayed kick-off to the second half at the same match."
The DFB faced further action after last night's win over Holland.
UEFA said in a statement: "UEFA confirms that it has opened disciplinary proceedings against the German Football Association (DFB) following last night's UEFA Euro 2012 Group B match between Germany and the Netherlands in Kharkiv.
"The DFB is charged with the setting-off of fireworks and the throwing of missiles by supporters.
"The UEFA Control and Disciplinary Body will deal with the case on Monday 18 June."