Goalkeeper Volkan Demirel also made a penalty save as Turkey moved to nine points, six behind Group A leaders Germany.
Arda, recently recovered from a groin injury, gave Guus Hiddink's side the lead after 28 minutes when he beat two defenders before slamming the ball into the far corner.
Gokhan made it 2-0 after 78 minutes but Austria wasted the chance to set up a nervy finale when Stefan Maierhofer's 84th minute penalty was saved after it had been awarded for a foul by Hakan Balta on Erwin Hoffer.
Turkey moved into second place in the group alhough Belgium will go back above them if they beat Azerbaijan later on Tuesday.
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