The Spaniard's first-half finish and the Belgian winger's clinical second ensure the Bianconeri's lead at the top of the table remains at 11 points
The Spaniard prodded home from close range in the first half to put the hosts in front, although he was fortunate to escape an offside flag following Lorenzo Insigne's cross.
Mertens sealed the win in the closing minutes with a well-taken finish to leave Juve's lead at the top at 11 points following Roma's win over Sassuolo.
The defending champions went into the match on the back of seven straight wins in the league and Inter's record points total of 97 looked very much in their sights, but Napoli's commanding display and win has put that in doubt.
Defeat for Juve - only their second in Serie A in 2013-14 - means their lead at the top of the table stands at 11 points after Roma won earlier in the day at Sassuolo, but Antonio Conte's men remain very much in line to secure a third successive title.
Conte's counterpart Rafael Benitez made the point of highlighting the two sides' differing revenues in the build-up and Juve's financial firepower was encapsulated by Italy international Pablo Daniel Osvaldo replacing the suspended Carlos Tevez in attack.
However, it was the hosts who looked more dangerous in the early stages and Buffon produced a crucial save after just six minutes, parrying away Callejon's close-range flick.
Marek Hamsik had a goal disallowed for offside a few moments later, but went close to netting legitimately in the 10th minute as Buffon acrobatically tipped his effort over following Henrique's cut-back.
The visitors finally tested Pepe Reina with 25 minutes on the clock, but he collected Stephan Lichtsteiner's tame left-footed shot with ease.
Juve's attacking threat continued to dwindle and they found themselves behind in the 37th minute, as Callejon directed Lorenzo Insigne's deep cross past Buffon, despite appearing to be offside.
After an inept first-half performance, Juve offered a little more from an attacking perspective in the second period, but Napoli still looked dangerous on the break and solid at the back.
Despite their improvement, Juve had to rely on Buffon once again to keep them in the game in the 60th minute, with the veteran palming Faouzi Ghoulam's free kick on to the roof of the goal.
Hamsik should have wrapped up the three points with 12 minutes to go as hit a gentle effort at Buffon, but Mertens made sure a few moments later, latching on to Goran Pandev's lofted pass before rifling into the net to secure a 2-0 win.