Napoli were let off the hook on on 40 minutes when Brignola's surge forward saw the ball worked to Berat Djimsiti, who could only find the side-netting when unmarked from 12 yards.
The Partenopei made the most of the reprieve by scoring their second on 47 minutes, Hamsik rifling Jose Callejon's pass across the face of goal into the net from close range.
Benevento were denied a penalty in the 56th minute when Kalidou Koulibaly brought down Andrea Costa, only for VAR to show that one of their players was offside during the build-up.
With 16 minutes to go, Mertens was brought down by a crunching Djimsiti challenge, forcing the Belgian to limp off the pitch.
The incident did not impact on Napoli's performance, however, as they secured all three points and leapfrogged Juventus back into first place.
BENEVENTO (4-3-3): Puggioni; Venuti, Djimsiti, Costa, Letizia; Cataldi, Sandro (Del Pinto 83'), Djuricic (Memushaj 67'); Brignola (Coda 63'), Guilherme, D'Alessandro
NAPOLI (4-3-3): Reina; Hysaj, Koulibaly, Albiol, Rui; Allan, Jorginho (Diawara 78'), Hamsik (Zielinski 69'); Callejon, Mertens (Rog 76'), Insigne