The hosts got off to a superb start on Wednesday as Mevlut Erding headed in a second-minute cross, catching Sweden completely off guard.
Fatih Terim's side were lacklustre for the rest of the first half and Sweden were unlucky not to draw level when Jimmy Durmaz saw an effort cleared off the line, before Pontus Wernbloom nodded just wide.
They did eventually equalise early in the second period when Ola Toivonen seized on a defensive error, but parity only lasted a few minutes before Olcan Adin headed Turkey's winner.
Following Sweden's 4-2 aggregate defeat to Portugal in the World Cup qualification play-offs, coach Erik Hamren called for his side to embark on a "fresh start", but things did not go exactly to plan.
Durmaz met Onur Kivrak's punched clearance with a half-volley on the edge of the area and the effort looked destined to find the net, but Gonul crucially hacked the ball away off the line.
That chance seemed to spark Sweden into life and they had their best opportunity three minutes before the break as Wernbloom connected with a left-wing cross only to see his header fly agonisingly wide.
The Turks began the second period with renewed determination and almost doubled their lead as Arda Turan's 30-yard strike hit the crossbar and Erding sliced the rebound wide with an acrobatic scissor-kick.
Sweden made the most of that let-off and they were level in the 54th minute as Zlatan Ibrahimovic's half-time replacement, Toivonen, pounced on a loose touch by Semih Kaya and coolly slotted past Kivrak.
They were only level for three minutes, though. Caner Erkin delivered a brilliant cross between the goalkeeper and the defence from the left flank and Olcan headed Turkey into the lead from the back post.
Sweden created some pressure in the final stages, but Turkey's lead was rarely threatened and they comfortably held on to win.
