Roy Hodgson's men were unable to break down the South Americans despite numerous chances, leaving the Three Lions boss with serious concerns before next summer's World Cup
The Barcelona forward scored three times in his country's last two FIFA World Cup qualification games as they plotted a successful route to the finals in Brazil, and he stole in to net a seventh-minute header ahead of Leighton Baines, who was given the nod ahead of Ashley Cole at left-back for England.
Chile's slick interplay regularly caused problem's for England's defence, but visiting goalkeeper Claudio Bravo was forced into sharp stops from Frank Lampard and Jack Wilshere in an enjoyably open first-half.
The usual flurry of substitutions after the break disturbed the game's flow as England's failure to locate the final pass undermined their efforts and, in injury time, Gary Cahill carelessly gave away possession and Sanchez produced a superb chipped finish to put gloss on the victory.
In the first of three friendlies before selecting his final 23-man squad for the 2014 FIFA World Cup finals in Brazil, England manager Roy Hodgson handed debuts to Celtic goalkeeper Fraser Forster and in-form Southampton duo Adam Lallana and Jay Rodriguez.
Chile were without key man Arturo Vidal, who suffered a thigh strain in Juventus's 3-0 weekend win over Napoli.
England started brightly but after Phil Jones and James Milner tested an uncertain-looking Bravo, opposite number Forster’s first act was to pick the ball out of his net.
Jones' block thwarted Charles Aranguiz, only for Sanchez to dive across Baines and head home when Jean Beausejour sent the ball back into England's box from the left.
Forster beat away Beausejour’s 14th-minute effort as a busy night shaped up for both goalkeepers - Bravo athletically turning Lampard’s deflected free-kick over the crossbar before fisting Jack Wilshere’s rasping left-footer away.
But England remained defensively unsettled by Chile’s pace and directness and, after Gary Medel wasted a free header, Beausejour offered an ill-fitting conclusion to a wonderful 31st-minute counter- by failing to get a shot off as Forster forced him wide.
Just as Chile’s passing game was starting to dominate, England produced their best move of the match in the 44th minute – Wilshere and Wayne Rooney combining to feed Lallana, whose shot was deflected past the far post.
Despite a flurry of corners early in the second period, England were chasing shadows once more as Chile weaved through their defensive efforts and Eugenio Mena's cross was fumbled by Forster.
The first contribution of substitutes Chris Smalling and Gonzalo Jara was to receive bookings for an altercation at an England corner with an hour played after Baines’ free-kick dropped wide via the wall.
By that time, regular substitutions had taken their toll on the contest but Sanchez was still on hand to provide a delightful finale.
He stole in deep into injury time as the visitors claimed an upset win.