The Sparta Prague midfielder latched onto a low cross from Pavel Kaderabek two minutes before the hour and fired beyond Tolga Zengin from 12 yards to give the visitors a Group A triumph in Istanbul.
Turkey started the match well and moved ahead in the eighth minute through Umut Bulut, but they were unable to turn further possession into goals and were ultimately punished.
Tomas Sivok levelled with a powerful header eight minutes after Bulut's opener, but the Czechs had to wait until the second half for Dockal to seal the win.
With Iceland emerging 3-0 victors in Latvia, the Czech Republic remain second in Group A with maximum points from their two matches, while Turkey are bottom after a second straight defeat.
A slow start to the match from the visitors was punished inside the first 10 minutes as Turkey, who controlled possession in the early exchanges, took the lead through Bulut.
Pavel Vrba's side had posed little in the way of attacking threat, although a marauding run from David Limbersky sparked them into life.
The full-back's charge down the left saw him find Tomas Rosicky in the penalty area, but the Arsenal midfielder's effort was blocked by Semih Kaya.
They did not have to wait long for a second goal, though, as Dockal capped a flowing move with a low finish from Kaderabek's cross after 58 minutes.
As tension grew inside the Sukru Saracoglu Stadium, the hosts battled in vain to find an equaliser.
Turan was beginning to have more and more involvement in proceedings but he was denied by Cech on two occasions just after the hour.
With time running out, Caner Erkin also had a chance to test the goalkeeper, but once again the 32-year-old Cech was more than equal to it to secure his side the win.
