The Partenopei will lock horns with the Bianconeri in the Coppa final after successfully scoring twice and keeping a clean sheet against Giuseppe Sannino's under-strength side
A Simone Vergassola own-goal and an Edinson Cavani header in the first-half was enough to comfortably cancel out the hosts' 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 who 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-hand 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 were aptly rewarded for their 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 further extended their 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 eventually managed to ride out the storm until half-time.
A less eventful second period was in order, as Siena were 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 their 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 team-mate through, but the Argentine ballooned his finish over the bar.
They could have paid the price for their 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-shot deep in injury time.
Fortunately for the hosts, they held onto their slender victory, and they will now face the Old Lady in the final of the Coppa Italia at the Olimpico, as they set their sights on landing a first trophy since 1987.