The match will take place on Saturday, June 25 at the Estadio Santa Laura Universidad SEK in Santiago.
It will be the first time Scotland have faced Chile, with the hosts using the match as preparation for their Rugby World Cup play-offs against USA after beating Canada last year in an Americas qualifying match.
Scotland A - in effect a team of fringe players - were last in action in February 2014 at Scotstoun in a match against England Saxons where Byron McGuigan scored Scotland's only try in a 16-16 draw.
Following the match in Santiago, Gregor Townsend's touring party will travel to Argentina for a three-Test series.
Head coach Townsend said facing Chile would be “a new challenge against a rugby nation on the rise”, adding: "Similar to the Tonga match last Autumn at BT Murrayfield, we will look to use a blend of youth and experience to start off the tour on a positive note.
"With the World Cup just around the corner, the four matches this summer will allow our players the chance to gain more game time and experience on the international stage.
"We always enjoy connecting with other countries and we are proud to be able to play Chile for the first time. It'll also allow us another week to acclimatise to similar conditions that we'll experience in Argentina such as playing at altitude and in a different time zone."