The DFB faces sanctions after fans threw projectiles from the stands, while the FPF could be penalised for the Iberians delaying the kick-off of the two sides' Euro 2012 meeting
During the game, which Die Mannschaft won 1-0, German fans threw paper at Portuguese players as they attempted to deliver corner kicks, and later some supporters ignited a smoke bomb.
The organisational body has confirmed it will investigate the actions of the German fans, as well as Portugal's part in delaying kick-off for the second half of the match.
In a statement to Goal.com, Uefa revealed the opening of disciplinary proceedings against the two organisational bodies.
"The German Football Association [DFB] is charged with the throwing of missiles by their supporters, while the Portuguese Football Federation [FPF] faces proceedings for a delayed kick-off to the second half," the statement reads.
"The Uefa Control and Disciplinary Body will deal with the case on Thursday 14 June."
Fans were repeatedly warned over the PA system that the throwing of projectiles could result in their ejection, sanctions for their team, and even abandonment of the match. Supporters tested the patience of referee Stephane Lannoy, but the official allowed play to continue to full-time.
The decision comes one day after Uefa pledged similar examination of Russian fan violence following their team's 4-1 win against Czech Republic.