The world number two took his 85th ATP World Tour title to end a long drought on clay dating back to the 2012 Madrid Masters, which was played on a slick blue surface.
"It's been a while since I won a title on clay," said the jubilant Swiss after receiving a hero's welcome all week in Istanbul. "It's been a pleasure playing here."
After winning the first set in just 33 minutes, Federer found it harder going in the second with Cuevas saving four match points.
"I think that the match deserved a third set," said Federer of his third title this season following victories in Brisbane and Dubai on hard court.
Federer has now won titles in 19 different countries.
(Reporting by Ece Toksabay; Editing by Martyn Herman)
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