And former Tottenham striker, Fernando Llorente, who spoke of wanting revenge for losing the Champions League final back in June, came off the bench to seal the points following a rare mistake from Virgil van Dijk.
The Merseysiders had their chances in a keenly contested affair, but Roberto Firmino headed wide and Mo Salah saw a rasping drive well saved by Alex Meret.
Jurgen Klopp's side lost 1-0 in the San Paolo at this stage last season and they found the Partenopei to be tough opposition once again, with Adrian producing a sensational second-half save to deny Mertens when the game was still scoreless.
The result means Napoli take second place behind Salzburg, who lead the pool after Matchday One courtesy of their thumping 6-2 victory over Genk.
Liverpool will now look to bounce back in Sunday's clash at Chelsea as the Merseysiders bid to extend their perfect start to their league campaign.
Deja vu for Liverpool in Naples. In a Group containing Champions League minnows in Genk and Salzburg, the matches between these two sides could be key to deciding who tops the pool. If that's the case, then this was a costly late lapse from Liverpool. Mistakes from Robertson and van Dijk continued their poor run of just three wins in 13 visits to Italy and extended their losing run in Group Stage matches to four. It will be particularly irritating for Klopp given that the Reds suffered a similar late loss in the San Paolo last year and have now failed to score on all three visits to the stadium.
Anfield was key to the Reds' progress to the Last 16 last term and it will be important to their hopes once more. Liverpool host Salzburg next up on October 2 in what is already looking like a must-win game. The holders will be expected to pick up the three points, but need to beware the Austrian side's Erling Braut Håland. The 19-year-old netted a hat-trick on a Champions League bow to remember against Genk. Liverpool will hope this is just a blip on what was always their toughest assignment in this group on paper.
MAN OF THE MATCH
Kalidou Koulibaly (Napoli). The defender was imperious at the back and was crucial to keeping Salah, Mane and Firmino at bay. Helped lay the foundations for the hosts to snatch the win late on.
NAPOLI: Meret 7, Di Lorenzo 7, Koulibaly 8, Manolas 7, Mario Rui 7, Callejon 7, Fabian 7, Allan 7, Insigne 6, Lozano 6, Mertens 7. Subs: Zielinski 6, Llorente 7, Elmas 6.
LIVERPOOL: Adrian 7, Alexander-Arnold 7, Matip 6, Van Dijk 6, Robertson 6, Milner 6, Henderson 7, Fabinho 7, Salah 6, Firmino 6, Mane 6. Subs: Wijnaldum 6, Shaqiri n/a.
match1112278Matchcast: Full match stats and commentarylive.aspxNone
7' - NAPOLI CHANCE. Fabian Ruiz lets rip with a 20-yard drive that Adrian can only parry. The Napoli man follows up to lash at the rebound but is thwarted by the keeper once more. It's nodded into the net from close range at the third attempt, but the flag is up for offside. Let off for the visitors.
44' - LIVERPOOL CHANCE. Firmino rises to meet Milner's left-wing cross but glances his header inches wide.
49' - NAPOLI CHANCE. That's a magnificent stop from Adrian. Mertens arrives at the back post to volley Mário Rui's lovely cross towards the goal, but the Reds keeper somehow palms it away.
55' - LIVERPOOL CHANCE. The hosts push too many forward and the away side break. Mane leads the charge. It's two on one but the Senegal forward overcooks his pass to Salah and a big opportunity is wasted.
65' - LIVERPOOL CHANCE. Salah seizes upon a dreadful miscue from Manolas, but sees his low, angled drive tipped past the post by Meret.
74' - LIVERPOOL CHANCE. Mane exchanges a slick one-two with Firmino on the left, but can't find enough power in his low shot to truly trouble Meret.
82' - GOAL! Napoli 1-0 Liverpool. Mertens lashes home the spot kick via a big hand off Adrian. The keeper almost got there.
90+2' - GOAL! Napoli 2-0 Liverpool. It's all over. Llorente latches on to an error from van Dijk and coolly slots it beyond Adrian.
Liverpool lost the opening match of a European Group game for the first time since 2002.
Liverpool are the first holders to lose an opening fixture the following season since AC Milan in 1994.
Liverpool have not won any of the last five away group fixtures, drawing one and losing four.