The Dutch, who needed just a draw to finish as the group champions owing to a better goal difference, scored in the 77th minute when Leroy Fer substituting Wesley Sneijder netted the ball by a superb header.
FINAL GROUP B STANDING
Netherlands: Played 3, Won 3, Goals For 8, Goals Against 3, Points 9
Chile: Played 3, Won 2, Lost 1, GF 5, GA 3 Points 6
Spain: Played 3, Won 1, Lost 2, GF 4, GA 7, Pts 3
Australia: Played 3, Lost 3, GF 3, GA 9, Points 0
Memphis Depay, who scored the winner against Australia in the previous match, sealed it for the men in orange in the injury time following a fantastic run from Arjen Robben.
The Dutch were without suspended Robin van Persie, who have scored three goals in two matches so far, in an otherwise dull contest.
The Netherlands will face the runners-up of Group A (comprising Brazil, Mexico, Croatia and Cameroon) in the pre-quarter final at Fortaleza on June 29 while Chile will take on the champions of Group A at Belo Horizonte on June 28.
Defenders Spain trounced Australia 3-0 in another inconsequential tie of Group B. Spain earned their first points of the tournament by winning this game but it was just for academic interest for they had already been knocked out by consecutive losses to the Netherlands and Chile.