Harry Kane and Jamie Vardy, who scored 49 Premier League goals between them this season, added one more each to their personal tallies as the Three Lions emerged victorious from the first of their three warm-up matches.
The hosts were playing their first home game away from Wembley since 2007, and they got off to a blistering start in Manchester as Kane gave them the lead after just three minutes.
The Tottenham Hotspur striker had already almost created an opening for strike partner Vardy when he collected Dele Alli's pass inside the area before confidently finishing into the bottom corner - his 32nd goal of the season for club and country.
Replays showed that Kane appeared to be offside for the goal, but Turkey quickly overcame the setback and began to ask questions themselves going forward.
In the absence of Wayne Rooney and James Milner due to club commitments, Kane was entrusted with the free-kick duties, and the goalscorer flashed one right across the face of goal with his first attempt.
Turkey levelled things up just a minute later, though, as Volkan Sen beat Hart to the ball down the left channel and chipped a pass over the keeper to Hakan Calhanoglu, who was left with a simple finish at the back post.
It was Turkey's first ever goal against England, ending a 10-match wait to breach the Three Lions' defence that stretches back to 1984.
Wilshere turned provider as England came close again shortly before the half-hour mark, swinging in a corner that Eric Dier flicked into the side-netting at the near post.
Babacan then made a routine stop to keep out another Kane effort, but it was Turkey who created the last chance of the first half when Mehmet Topal rose to meet Calhanoglu's free kick, only to nod it high and wide.
England made another bright start to the second half and had a shooting opportunity in the opening seconds when the ball broke kindly for Alli, but his effort deflected straight into the arms of the keeper.
Turkey continued to look dangerous at the other end of the field, however, and came close twice in quick succession through Tosun, who first put a header narrowly past the post before collecting the ball with his back to goal on the edge of the box and firing a low effort just wide on the turn.
England threatened from a set piece themselves moments later when John Stones rose to meet Kane's free kick, but he couldn't get enough on his header to trouble Babacan.
The way the hosts were defending set pieces would have concerned Roy Hodgson, though, and they gave up another chance shortly after the hour mark when Hakan Balta's header across goal was hooked back into a dangerous area before being bundled behind by Danny Rose.
England were handed a glorious chance to move back in front with just under 20 minutes remaining when Vardy pounced on an error from Topal to race through on goal, before going down under the challenge of the Turkey skipper inside the area.
The referee pointed to the spot and Kane stepped up to take it, but he blasted an effort off the post and wide, becoming the first England player to miss a penalty for six years.
It would not prove to be a costly miss, though, as a mix-up from Babacan and Ismail Koybasi saw Gary Cahill's header spill loose inside the area, and Vardy was first on the scene to convert the rebound from close range.
It was a third England goal in as many games for the Premier League winner, who had switched from a wider role into a more central position during the second half as Hodgson experimented with different formations.
It could have been even better for England in the closing stages too as Vardy turned provider, latching on to a long ball over the top and finding Kane, only for the Tottenham man to slip while shooting as his effort went past the post.
Turkey almost rescued a draw in the dying minutes, though, and it took a fine save from Hart down low to his right to prevent substitute Olcay Sahan from maintaining the visitors' 13-match unbeaten streak.
Ultimately, though, it was a first defeat since November 2014 for Fatih Terim's side, while England have now won 10 of their last 11 games on home soil.