Gattuso led Napoli to its sixth Coppa Italia triumph in his first half-season at the club in 2019-2020, and talks of a new deal were rife earlier this season.
Yet those discussions have made way for reports of Gattuso's imminent departure and, despite a spirited second-half showing sparked by Hirving Lozano's 53rd-minute goal, his time might be up.
Without Kostas Manolas or Kalidou Koulibaly, Napoli's defence was carved open in the first half – Duvan Zapata integral as he scored the opener and twice set up Matteo Pessina, whose double sent Atalanta into a final against last season's runners up Juventus.
After drawing 0-0 in the first leg, Atalanta threw away a three-goal lead against Torino on Sunday and might have conceded early on this time had Lorenzo Insigne directed a dipping volley on target.
But it was Atalanta who hit the front when Zapata arrowed a brilliant 10th-minute shot into the left-hand corner from 25 yards out.
Zapata turned provider six minutes later, the Colombia striker playing a crisp first-time pass into the path of Pessina to round off a slick team move.
Atalanta could have had a third prior to the break if Zapata had kept a close-range prod down.
With nothing to lose, Napoli came out rejuvenated after the break, and had their rewards when Lozano turned in at the second attempt following Pierluigi Gollini's save.
Zapata should then have restored Atalanta's two-goal lead, yet failed to keep his header on target after meeting Josip Ilicic's corner.
His profligacy may have proved costly, but Gollini made a superb stop to deny Victor Osimhen, and Pessina ultimately wrapped up the win with a deft close-range finish to book Atalanta's place in the final.