After opening the scoring through an early try from Rodrigo Fernandez in Sunday's match, the South Americans, the lowest-ranked team at this World Cup, added another from Alfonso Escobar with Santiago Vila slotting over the conversion.
But Japan made the most of Chile's two yellow cards to prevail with a brace by Amato Fakatava and other tries from Jone Naikabula, Michael Leitch, Ryoto Nakamura and Warner Dearns, all six being converted by Rikiya Matsuda.
A rousing rendition of the Chilean national anthem was followed by a spirited start from the first World Cup debutants since Russia in 2011, and then a dream try in the sixth minute, manufactured with Latin flair and finished off with a dollop of good fortune.
Fullback Inaki Ayarza broke through two tackles to set up the opportunity, but captain Martin Sigren looked to have spoilt it when the ball was knocked out of his hand in the tackle.
But it went backwards and quick-thinking five-eighth Fernandez pounced on the loose ball, dribbling it forward and then diving on it to dot down. A check by the TMO confirmed the try to the delight of the capacity crowd.
Chilean euphoria lasted less than 120 seconds as they dropped the ball from the kick-off, allowing Japan to score as lock Fakatava showed a fleetness of foot to burst through and sprint away from the defenders for a quick reply.
Basic errors betrayed Chile's naivety and a late tackle from Matias Dittus on fellow prop Koo Ji-won meant a 10-minute spell in the sin bin, during which time Japan went in the lead on the half-hour mark as winger Naikabula stretched over for their second try.
Sigren was also binned after head contact in a tackle on Kotaro Matsushima and with the numerical advantage Japan were able to maul over on the stroke of halftime as Fakatava claimed his second try and stretched the lead to 21-7.
But the rookies continued to resist as Escobar burst over for a 48th minute try to fire up the crowd and cut Japan's lead to nine points.
That was as good as it got for the gutsy Chileans, with Leitch scoring Japan's fourth try in the 53rd minute, centre Nakamura the next 10 minutes from time and 21-year-old Dearns used all of his two-metre frame to stretch over and score at the end of the game.
