The move had been mooted for several weeks, with Napoli said to have identified Fabian as a primary target in the event of Jorginho leaving after impressing in his first full season in La Liga.
Still just 22, Fabian forced his way into the first team last term, catching the eye with the ability to produce both creative and combative performances.
With Jorginho set to join Manchester City , Fabian said in June that a move to Napoli was likely and both clubs confirmed the transfer had been completed on Thursday as the midfielder signed a five-year deal.
A Spain Under-21 international, Fabian has just one full season of top-flight football under his belt.
He played 34 times in La Liga during the 2017-18 campaign, scoring three goals.
The Betis academy product joins Spanish compatriots Raul Albiol and Jose Callejon in Naples.
In June, Goal revealed that City were closing in on a deal worth around £50 million (€56.9m $66m) for Jorginho , with Napoli then leaving the 26-year-old out of their pre-season squad as they began to plan for a future without the Brazilian.
Jorginho was a key part of Napoli's Serie A title challenge last season and played 39 times in all competitions for the club, scoring four goals.