It was the sixth European Tour win of Fernandez-Castano's career. The 31-year-old Spaniard's biggest previous victory came at last year's Singapore Open.
He hit a solid shot out of the rough following an errant tee shot and birdied the final hole of the Royal Park I Roveri course outside Turin, finishing at 24 under.
"It felt like match play out there and I'm delighted to have come out on top," Fernandez-Castano said. "It feels very special to win this tournament again. I knew it would have to be a low round to win today and so it proved. The putts were going in today."
Mulroy fell behind after a bogey on the 17th.
The Ryder Cup will be held in two weeks at Medinah Country Club outside Chicago.
The third Ryder Cup player in the field, Italy's Francesco Molinari, shot a 65 -- his best round of the week -- to finish at 10 under.
Europe captain Jose Maria Olazabal also finished with a 65 to end the week at 7 under.