Brazilian Reginaldo and Gaetano D'Agostino scored the goals to give Siena a semi-final, first leg victory although it may live to rue Emanuele Pesoli's late own goal.
Napoli may still be favourite to progress ahead of next month's second leg in Naples but Siena can be well pleased with their work.
The visitors played a full-strength side while the Serie A strugglers rested several first choice players.
And yet they had more determination and cohesion as they put one foot in the final and a possible glamour tie against one of the country's heavyweights.
Juventus won by the same score away to AC Milan in the first semi-final, first leg.