The Partenopei will feature in their first Coppa Italia final since 1997 after successfully scoring twice and keeping a clean sheet against Giuseppe Sannino's side.
A Simone Vergassola own goal and Edinson Cavani's header in the first half were enough to comfortably cancel out the home side's deficit against the Tuscans, having come into the match at a 2-1 disadvantage from the first leg a fortnight ago.
Unsurprisingly, it was Walter Mazzarri's outfit which started the strongest. Cavani looked hungry from the first whistle, but he uncharacteristically blazed over Ezequiel Lavezzi's visionary cut back at the far post from a matter of yards out.
But just seven minutes later, Napoli took the lead, albeit in slightly fortuitous fashion. Lavezzi's curling free kick from the right side was met by Simone Vergassola, who flicked the ball into his own net.
However, Siena almost hit back instantly. A delicious ball from Marcelo Larrondo almost dropped for Daniele Mannini, but the midfielder was beaten to the finish by Paolo Cannavaro, who intercepted in last-ditch fashion at the far post.
Nonetheless, Napoli pressed on and was aptly rewarded for its efforts on 14 minutes, following a lightning quick counterattack. Gokhan Inler was the instigator, finding an onrushing Marek Hamsik, who crossed the ball onto the head of Cavani for 2-0.
Napoli could have extended the lead, but a pair of sizzling volleyed attempts from Inler and Cavani were wonderfully tipped away by Zeljko Brkic in the Siena goal, as the Bianconeri managed to ride out the storm until halftime.
A less eventful second period was in order, as Siena was determined not to concede for the remainder of the encounter. Moments of discontent were also heard as Napoli supporters expressed their frustrations at their side making hard work of booking a place in the final.
Lavezzi was presented with a golden opportunity to make it 3-0 with 12 minutes to go, as Hamsik expertly skipped past Claudio Terzi and threaded his teammate through, but the Argentine ballooned his finish over the bar.
The team could have paid the price for its profligacy at goal, but Hugo Campagnaro was on hand to deny Franco Brienza from pulling the trigger in the box, while the Siena forward almost stunned Morgan De Sanctis with a cross-cum-shot deep in injury time.
Fortunately for the home side, it held onto the slender victory, and will now face the Old Lady in the final of the Coppa Italia at the Olimpico, as the team sets its sights on landing a first cup trophy since 1987.
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