Nadal held a 6-1, 3-0 advantage Saturday when Lopez decided he could not continue.
"He (was) playing very well," Nadal said on the ATP Web site.
"This morning when I woke up, I had an infection in my right foot," Lopez said. "It was painful during the match."
Sixth-seeded Nikolay Davydenko of Russia won Saturday's other semi 4-6, 6-4, 7-6 (7-1) over second-seeded Novak Djokovic of Serbia.
Sunday's Nadal-Davydenko winner will collect a $616,500 champion's check.
Nadal, a six-time major tournament champion, is 4-2 lifetime against Davydenko, and will attempt to win his sixth title of 2009.