Simone Verdi and Daniele Rugani put the visitors in complete control but Rafael Benitez's men nicked a point thanks to Duvan Zapata and Jonathan de Guzman
The Partenopei produced a dire first-half performance and were fortunate that they were only trailing to a solitary strike from Simone Verdi at the break.
Empoli deservedly doubled their advantage through Daniele Rugani early shortly after the restart but that goal belatedly sparked Napoli into life, with Duvan Zapata halving the home side's deficit before Jonathan de Guzman restored parity with 18 minutes to go.
Napoli poured forward during a frantic finale but were unable to find what, in truth, would have been an undeserved winner.
Indeed, Rafael Benitez's men had been atrocious for an hour and were particularly poor during the first half, getting caught cold on the break just 19 minutes in, when Verdi coolly slid the ball past Rafael after being put in on goal by Massimo Maccarone.
The latter should have made it 2-0 when the visitors pounced on a misplaced pass from Jorginho but the former Middlesbrough forward fired wide.
Francesco Tavano was then presented with an excellent opportunity to extend the visitors' advantage but the 35-year-old striker did not even force Rafael into a save after being put clean through on goal.
However, Rugani finished emphatically when a corner dropped for him eight minutes into the second half, the defender controlling the ball with the outside of his right foot before slamming it home from six yards out.
Napoli appeared dead and buried but Zapata, who netted an injury-time equaliser at Sampdoria on Monday, handed them a lifeline in the 67th minute when he headed home from a corner.
The Partenopei were level just five minutes later when a a Jose Callejon cut-back was deflected into the path of De Guzman, who made no mistake from 10 yards out.
The Dutchman very nearly nicked a winner in the dying seconds but his volley was well saved by Luigi Sepe, who is on loan to Empoli from Napoli.
As it was, though, Napoli were forced to settle for a third successive draw in Serie A and their fourth in all competitions.