Fognini, who helped lead Italy over Argentina last week in the opening round of the 2014 Davis Cup, fought off the third-seeded Spaniard 6-4, 1-6, 7-6 (7-5) on the clay courts of Vina del Mar.
He'll seek his third career championship against Argentina's Mayer, who reached the final with a 7-6 (7-2), 6-3 decision over Colombia's Santiago Giraldo.
The unseeded Mayer will be playing in his first career title match.
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