The Dutch, who also beat Germany 2-0 in the group stage, twice came from behind in their third final at this level to avenge a 2-1 defeat by the Germans in the 2009 showpiece.
Samed Yesil gave Germany an early lead after powering past two defenders and they seemed on course to repeat their 2009 success when Okan Aydin made it 2-1 with a spectacular long-range effort, shortly after De Vilhena had equalised.
The talented Dutch striker levelled again just before the interval to set up a one-sided contest in the second half.
Netherlands took control of the game when winger Memphis Depay scored after a dazzling solo run and defender Terence Kongolo made it 4-2 with a close range tap-in.
Arsenal prospect Kyle Ebecilio, one of the tournament's outstanding players, put the icing on the cake in the closing stages, drilling his shot from 13 metres into the top corner after a flowing team move.
The top six teams from the eight-nation tournament qualified for the June 13-July 10 Under-17 World Cup in Mexico.
Apart from Netherlands and Germany, Europe will also be represented by England, Denmark, Czech Republic and France.
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