The Argentine's low drive from the edge of the area was fumbled by goalkeeper Alban Lafont in the 69th minute as Atalanta completed a 5-4 aggregate win to continue their remarkable season.
Luis Muriel put Fiorentina ahead after three minutes, slipping the ball past Pierluigi Gollini after being sent clear by Federico Chiesa's incisive pass.
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Atalanta levelled 11 minutes later, Josip Ilicic converting a penalty after Gomez went down under a challenge from Federico Ceccherini.
Atalanta, who will meet Lazio in the final on May 15 in Rome, have won the competition once, in 1963 -- the Bergamo club's only major trophy. Fifth in Serie A, they are also challenging for a place in next season's Champions League.
The defeat effectively ended Fiorentina's season as they are 11th in Serie A with no realistic chance of qualifying for Europe and are under no threat of relegation.
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