The prince joined three of the 94 families who were left homeless in the community of El Vergel in the April incident.
The blaze left 15 people dead, damaged or destroyed 2,900 homes and left more than 12,500 without a roof over their head.
In casual clothing and sneakers, Prince Harry toured the area for more than two hours and checked in on rebuilding efforts. He also chatted with victims and later posed for pictures with the families.
On Friday, the prince, 29, met briefly with President Michelle Bachelet at the ornate La Moneda palace in the capital Santiago.
Harry, fourth in line to the British throne and an army captain, arrived in Santiago on Thursday night on a scheduled flight after an official visit to Brazil, where he saw the England football team play out a 0-0 bore draw against Costa Rica on Tuesday in their last game of a disappointing tournament.
The prince recently made headlines with his party-going antics at a wedding in Memphis, and there has been intense speculation about his private life after his split from girlfriend Cressida Bonas.