The South Americans pressed high and forced the Netherlands into making mistakes early on, but their only chance on goal was a Felipe Gutierrez header from close range that went wide.
The Dutch were looking to play on the counter-attack, and the pacey Arjen Robben nearly scored with a solo run from the halfway line. The Bayern Munich winger beat two defenders and then shot from the edge of the area, only for his effort to drift wide of the far post.
The second half was limited in chances, much similar to the first, until a great run from substitute Memphis Depay, beating Gonzalo Jara with a lovely bit of skill, before shooting a long-range effort that forced Claudio Bravo into a great save.
The following set-piece brought the first goal of the match, through Norwich City midfielder Leroy Fer. An outswinging cross from the right by Daryl Janmaat was met by Fer, who was unmarked just eight yards out, and finished with class into the side of the net.
Chile pushed for the equaliser, and was hit on the break in the 92nd minute when Robben set up Depay to score from close range.
The 2-0 win means the Netherlands secure top spot of Group B, whilst Chile will have to settle for second place and a last 16 match that is likely to be against hosts and favourites, Brazil.