With 10 goals in his last seven matches, the 27-year-old Colombian is in place to have his best season as a professional, topping the 16 goals he scored in 2012-2013 with Argentina's Estudiantes, reports Efe news.
Atalanta dominated for much of the contest at Sardegna Arena in Cagliari on Monday night, but the first goal came only in the 88th minute when Zapata headed in.
Four minutes later, he assisted on Mario Pasalic's goal in stoppage time to seal the victory.
Atalanta's opponent in the quarter-finals will be Juventus, who are in pursuit of a fifth consecutive Coppa Italia.
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