In a stage scoped out for a bunch sprint finish, Polish rider Niemiec disagreed with his three other escapees when they surrendered after the gap fell to 40 seconds.
He attacked on a descent and eventually increased his advantage to a maximum of three minutes, a longer gap than the breakaway group established.
Finishing just 16 seconds ahead slowing down as he ascended the climb to Sultanahmet Square near the Blue Mosque towards the finish, team director Daniele Righi said his win wasn't a total surprise.
"We’re all very happy Niemiec could win the stage in this unusual way for him, who’s more used to be competitive in mountains stages.
"However, Przemyslaw realised a very impressive performance, demonstrating his skills and his determination.
We’ll try stage by stage to go on in the same way we started the Tour of Turkey."
The race started out neutralised after crashes affecting stage favourites Carlos Barbero (Caja Rural-RGA), Andre Greipel and also Davide Rebellin (CCC Sprandi-Polkowice).
Barbero was seen clutching his collarbone and abandoned the race. Greipel's team said the crash affected his left calf, however, he still finished the 129km stage.
