Ferrer, the tournament's top seed, survived a 4-6, 6-2, 7-6 (7-2) battle with Almagro, who was seeded fifth.
The title was Ferrer's sixth on the men's tour.
"I'm very happy for having won the title in Valencia, at my club, in front of my family and friends," Ferrer said. "It just feels incredible to have won at home."
Ferrer's win was worth $93,000.