The victory was courtesy of a brace from Chelsea midfielder Mateo Kovacic.
Courtesy of the win secured in Turkey on Tuesday, they have moved up to the second spot in Group D, pushing Turkey to the third spot.
Before the qualifying round, Turkey was topping the log after winning on matchday one in the Wales and Latvia group.
Three days ago, Croatia was held to a 1-1 draw by Wales, while Turkey defeated Armenia.
Wales occupies the summit of the log after beating Latvia 1-0. They lead the group by four points on goal difference from Croatia, with Turkey third with three.
Kovacic opened the goal account in the 20th minute as s he left Turkey goalkeeper Mert Gunok motionless when he scored from close range. The Chelsea midfielder got the opportunity to punish their host following a failed attempt by the defense to clear the ball.
He got his brace just before halftime as he tapped home a rebound after Gunok saved Mario Pasalic’s effort.
Turkey had started brightly, creating better chances early on, but they were kept out by Dominik Livakovic, who made some exceptional saves.
They suffered another blow when captain Hakan Calhanoglu had to come off in the 36th minute due to an injury.
After failing to impress in the 2020 edition of the European championship, Turkey, who reached the Euro 2008 semi-finals, are looking to qualify again. They left the last edition pointless, losing all three games and scoring one goal.
They can turn the tide in the next international break when they play Latvia and Wales.
Wales also hopes to qualify for another European championship, having qualified for the last two international competitions.