Esteban Paredes got the only goal of the game for the South Americans as his far-post header on the half-hour mark secured the spoils.
The home side, who are in the same group as Honduras, Spain and Switzerland in South Africa, made a confident start and Linfield goalkeeper Alan Blayney was forced into an early save as Marco Estrada shot straight at him.
Blayney was called into action soon afterwards as he raced off his line to deny Gonzalo Fierro.
But Paredes gave Chile a deserved lead as Matias Fernandez's corner from the right came through to him, with his header squeezing past Blayney and into the net.
Northern Ireland looked to hit back quickly as some neat build-up play released teenager Johnny Gorman, but he was unable to get his shot away as a heavy touch allowed two Chile defenders to slide in and take the ball.
The hosts continued to look dangerous and Mark Gonzalez dragged a weak shot across goal when he ought to have done better, before Gorman spurned an excellent chance to get Nigel Worthington's side back on level terms.
Rory Patterson did well to put the Wolves youngster through, but he blazed wildly over the bar with only Miguel Pinto to beat.
Worthington made four changes at the break as Michael McGovern, Roy McArdle, James Lawrie and Kevin Braniff all came on, but they continued to struggle as Chile dominated possession.
Substitute Fabian Orellana blazed wildly over the crossbar from the edge of the area before the referee turned away a strong appeal for a penalty after Paredes appeared to be clumsily tripped in the area by Andrew Little as he burst through on goal, with the official ruling that the Rangers man had won the ball.
Estrada then produced a stunning left-footed strike from fully 30 yards in injury-time, forcing McGovern to make an athletic save to keep out the powerful shot.
Chile move on to face Israel tomorrow night, while their final warm-up game sees them face New Zealand two days before the World Cup begins.