Victor Osimhen fired blank for Napoli and was replaced by Andrea Petagna in the 79th minute as Atalanta claimed a 3-1 win in the reverse fixture of the Coppa Italia semi-final tie on Wednesday night.
Atalanta will now face Juventus in the Coppa Italia final thanks to two goals from Matteo Pessina.
After a goalless first leg, Duvan Zapata fired Atalanta into the lead from 25 yards – and the striker was involved in all three goals.
He set up Matteo Pessina for their second goal after only 16 minutes.
Hirving Lozano gave Napoli hope but then Pessina poked home the clinching goal after a fine passing move.
Atalanta – who lost the 2019 final to Lazio – have only won one major trophy in their history, the 1963 Coppa Italia.
They have been one of Italy’s top sides in recent years – scoring more goals than anybody else in Serie A in each of the last two seasons – and reaching the Champions League quarter-finals in 2020.
Juve – who beat Inter Milan 2-1 on aggregate – await them in the final on May 19.