Following a disappointing 120 minutes in Hamburg, the drama of spot-kicks saw Joao Felix miss with his attempt, as Theo Hernandez kept his composure to fire in the decisive effort.
Bruno Fernandes did not take part in the penalties, after scoring one against Slovenia in the previous round, after he was substituted, while Diogo Dalot, who netted for United in the Emirates FA Cup semi-final shootout with Coventry City, was not introduced off the bench.
It means the first semi-final is set, with Spain taking on France on Tuesday, and the other two quarter-finals, England versus Switzerland and Turkey versus the Netherlands, take place on Saturday,