A late goal from Jesus Navas prevented a shock defeat for the world champions as Eduardo Vargas' double had looked to have consigned them to defeat
Sloppy defending in the fourth minute allowed Eduardo Vargas to give the South Americans an early lead and, following Roberto Soldado's equalizer, the Gremio forward restored his side's advantage just before halftime.
Jorge Sampioli's troops looked set to have secured an unexpected friendly triumph on neutral soil, but Manchester City winger Navas saved Vicente del Bosque's men's blushes with a close-range leveler two minutes into added time.
Del Bosque made a host of changes from the side that beat Finland 2-0 in a World Cup qualifier on Friday.
He was without Isco (ankle) and David Silva (thigh), while Victor Valdes was given the nod in goal ahead of Iker Casillas, who earned his 150th cap in Helsinki.
Nacho Monreal, Santi Cazorla and Soldado were also brought in to the starting lineup.
Chile named all three goalscorers from its Venezuela clash last week as Vargas, Marcos Gonzalez and Arturo Vidal lined up in a strong starting XI.
The visitors seized the early initiative when Vargas latched onto Mauricio Isla's flicked pass before slotting the ball past Valdes from 12 yards.
Spain was exposed at the back again midway through the half, when Valdes had to scramble Alexis Sanchez's cross-cum-shot behind for a corner.
Claudio Bravo almost cost his side at the other end when the goalkeeper allowed a tame backpass to roll under his foot and out for a corner, from which Spain failed to threaten.
But despite struggling to find its rhythm, Spain did manage to conjure a leveler nine minutes before the break.
Tottenham striker Soldado was the beneficiary of Alvaro Arbeloa's pinpoint delivery, heading home from six yards for a barely deserved equalizer.
But after Cesc Fabregas' cross hit the post, Spain was cut open again on the stroke of halftime.
Vargas turned Raul Albiol and finished into the bottom corner to send Sampaoli's men into the break with the lead.
Andres Iniesta and Navas were brought on for Fabregas and Xavi as Spain looked to turn things around in the second period, having looked nothing like the side that had managed five clean sheets in its past six matches.
Spain began to grow into the game, enjoying long spells of possession as Chile seemed content to try to contain it.
Cazorla fed Pedro down the down the left but his cross deflected off Gary Medel, giving Soldado no chance to capitalize.
Valdes was replaced around the hour mark, making way for Pepe Reina, who was called into action when Mauricio Isla raced through and the Napoli loanee had to sprint out to deny him.
Del Bosque introduced Alvaro Negredo to the action in place of Soldado and the Spaniards pressed again, winning a free kick on the edge of the box as Cazorla was sent tumbling, resulting in a yellow card for Vidal.
But Iniesta's strike was straight at the wall and when Navas could only sting Bravo's palms with a close-range strike, Spain's frustration was evident.
With its illustrious opponents failing to fire on all cylinders, Chile looked set to record its first win over Spain, but Navas had other ideas, poking Pedro's cross home from close range to ensure that the world and European champions have lost only one of their last 30 matches.