Damien Hoyland got the opening score to mark his return to Scotland colours after while George Horne added two more.
Hoyland crossed again before half-time and grabbed his third try early in the second period. However Scotland were unable to add to stretch that lead against a hard-working Chile side. The hosts were finally rewarded for their efforts through a fine try from Santiago Edwards.
Scotland managed to put a bit of gloss on the score when Rufus McLean and Ali Price went over in the closing minutes as the Chile team tired.
Gregor Townsend's side will now play Argentina on the first three Saturdays in July.
"We got a really tough workout," said Townsend. "We had to fight in that second half to keep Chile out and they did eventually score a try.
"We've got some areas of our game we know we'll have to work on more next week but there were a lot of positives. The way we played in the first half, the way some young players integrated into the team, and the way we took our opportunities was great to see. Our strong finish was also pleasing.
"Chile are a very good rugby team. They are physical and committed with some very good rugby players. They grew as the game went on so that's a sign of a team that's improving and learning what is working from them on the field."
Earlier in the day Scotland U20 went down to a heavy defeat to Wales at Treviso's Stadio di Monigo in the first of the Six Nations Summer Series Pool B matches.
The young Scots went down 45-15 with their points coming from a try from Gregor Hiddleston and a double from Patrick Harrison.