The 30-year-old Verdasco ended a six-match losing streak in tournament finals. He also reached the doubles final and had been on the court six hours longer than Almagro going into the final.
"I'm so tired I don't know if I can talk so much," said Verdasco, seeded fourth.
Almagro had a walkover in the semifinals when Sam Querrey pulled out because of back injury.
The third-seeded Almagro reached set point five times against Verdasco's serve in the ninth game of second set, but couldn't convert. He also up a mini-break in the tiebreaker before Verdasco rallied.
Almagro also finished second last year, losing to John Isner. Almagro has won all 12 of his titles on clay.
"You are never happy when you lose a final," Almagro said. "I had my chances. But I credit Fernando."