Edinson Cavani broke the deadlock after just over an hour's play from the penalty spot before Marek Hamsik made the trophy safe on the counter-attack with seven minutes remaining.
Substitute Fabio Quagliarella's straight red card in the final minute of regulation time for an elbow to the face of Salvatore Aronica added further misery as club legend Alessandro Del Piero's final game for the Old Lady ended with the first blemish on its 2011-12 record.
Napoli coach Walter Mazzarri may well lose the likes of Cavani and Ezequiel Lavezzi in the summer, but the Coppa victory ensures they go out with a winner's medal - the Naples outfit's first success in the tournament since 1987.
It was Napoli who started brightest and they almost had the opening goal with just 70 seconds on the clock.
Defender Hugo Campagnaro attacked down the right and combined well with Christian Maggio before sending a peach of a cross towards the far post, where Juan Zuniga’s header forced a point-blank parry from Marco Storari.
After weathering the early storm for a quarter of an hour, the Serie A winners began to force their way into the game, with Claudio Marchisio forcing a great save from Morgan De Sanctis on 18 minutes.
The Napoli goalkeeper was called into action again in stoppage time at the end of the first half when Del Piero sent a scorching 25-yard free-kick on target, forcing another fine stop from his fellow veteran.
The Partenopei began the second 45 with the same vigour as the first, and Juve were left frustrated as a number of decisions went against them.
They could have no arguments on 62 minutes, however, when Lavezzi caught the defence napping and lured a foul from Storari, winning his side a spot kick.
Cavani coolly despatched from 12 yards and the Naples club had drawn first blood.
But as the Turin side applied more pressure, gaps were opening at the back and the Neopolitans came close to exploiting them time and time again – until they finally managed it in the 83rd minute.
Substitute Goran Pandev – on the winning side in every Coppa final since 2009 – threaded the perfect ball through to Hamsik and the vice-captain secured victory with a cool finish from 12 yards across Storari.
Though Quagliarella’s dismissal for the Aronica elbow after the two engaged in a tussle at a set-piece was an unfortunate footnote on the contest, nothing could drag Napoli out of party mode as Paolo Cannavaro held aloft the Coppa trophy after the final whistle.