The Turkish rider rode away from the lead group in the final five kilometres, a steep uphill section, with Turkish fans deliriously running alongside his bike waving flags.
Cofidis duo Yohann Bagot and Nicolas Edet were second and third, 18 and 23 seconds behind Sayar respectively.
Konya Torku Seker Sport rider Sayar was third after stage five but now leads by 41 seconds on GC after the 177km stage from Bodrum to Selçuk - and is the hot favourite to claim overall victory ahead of the two shorter stages which conclude the stage race.
Previous leader Ethiopean Natnael Berhane (Europcar) was 43 seconds off the winner's pace, yet just holds on to second spot overall by three seconds from Bagot.
The first break of the day came after 40km, featuring 14 riders, but many were reeled in by the riders. That left Christian Delle Stelle (Bardiani) and Aldo-Ino Ilesic (UnitedHeatlhCare) out in front: at one point they built a lead of almost 10 minutes.
With neither rider known as a climber, it was a surprise to see them attack on such a hilly stage. The gap was steadily eaten away until the pair was caught with 30km to go, ahead of two final climbs.
Kevin Peeters (Crelan), Anthony Delaplace (Sojasun) and Rafael Andriato (Vini Fantini) attacked on the penultimate climb but were quickly caught, while Berhane picked up a puncture - the day was littered with them - at the summit.
There were a couple of brief solo attacks after the descent, both of them quickly absorbed. Berhane looked to be in a good position before the start of the final hill: he and Edet went with Sayar as he attacked, but the Turk dropped them both and stayed well clear to take a jaw-dropping win.
Saturday is a 124km undulating stage to Izmir, with a 121km circuit stage around Istanbul finishing matters off on Sunday.