It was Australia who opened the scoring after just nine minutes when Josh Brillante collected possession just outside the box before bending an effort into the bottom corner.
El Salvador were level less than 10 minutes later, however, when Diego Coca capitalised on uncertainty in the Australian defence before converting from close range.
Jose Pena completed the turnaround for El Salvador in the first period when the forward pounced on a loose ball inside the box before finding the bottom corner.
Pena came close to adding his second of the match just past the hour mark, but the youngster's effort was always moving wide of the post.
Brillante continued to provide the main outlet for Australia, but he could not add this third goal of the tournament as El Salvador held on for all three points.
Next up for El Salvador is a clash with Colombia on June 28, while Australia face hosts Turkey on the same evening.