The match, moved to December to accomodate Napoli's Champions League play-off commitments last August, was pushed into extra time after Gonzalo Higuain hit a 68th-minute leveller to cancel out Carlos Tevez's early opener for the Serie A champions.
The Argentinian duo went on to complete a brace apiece in extra time, forcing the match to be decided by a dramatic series of spot-kicks.
Juventus goalkeeper Gianluigi Buffon got the Serie A champions off to a great start when he palmed Jorginho's shot on to the upright, only for Tevez to hit the post despite sending Rafael the wrong way.
At 4-4, the match went to sudden death, and after Walter Gargano and Leonardo Bonucci scored their attempts, Juve scented victory when Buffon beat away Dries Mertens' effort.
However Giorgio Chiellini then sent his weak penalty straight to Rafael, and both Jose Callejon and Roberto Pereyra then missed too.
Kalidou Koulibaly put Napoli within sight of their first Super Cup since 1990 - when Diego Maradona's Napoli thrashed Juventus 5-1 - when he smacked his penalty in off the inside of the post.
And the Cup finally went to Rafael Benitez's men when Rafael pulled off a great save to deny Simone Padoin.