Almagro, a 12-time winner on the ATP World Tour ranked 20th in the world, reached the final for the second straight. He lost the 2013 final to John Isner.
Verdasco has five career titles, all on clay.
Querrey beat Dustin Brown on Friday night and appeared to be fine, but woke up with lower-back spasms.
"It didn't affect me at all my match," Querrey said. "But I woke up unable to bend forward or arch (my) back. We've been trying to loosen it up for three hours. I feel terrible . . . my first semi in a while and I really wanted to play. But (Almagro) was going to beat me (6-0, 6-0)."