Salzburg prevented Napoli from becoming the first team to qualify for the Champions League last 16 on Tuesday as the Italian side settled for a 1-1 draw in Naples.
Norwegian teenage striker Erling Haaland put the Austrians ahead from the spot after 11 minutes before Mexican Hirving Lozano grabbed an equaliser just before the break with his first goal at the San Paolo stadium.
Liverpool's win over Genk at Anfield ensures the reigning European champions go top of Group E at the expense of the Italians, with nine points from four games.
Napoli are still well on course to qualify as they are second with eight points, four points ahead of Salzburg, with Belgian side Genk on one point, with two games to play.
"It's a bit of an unlucky time for us," said Napoli captain Lorenzo Insigne.
"We tried everything. It's a great performance but we didn't manage to score enough.
"We have to look up and keep working. If we play like tonight soon the success will return."
Carlo Ancelotti's side have been struggling in the league, slipping to seventh in Serie A after taking only two points from their last three games.
Club president Aurelio De Laurentiis had ordered the team to be confined to their training camp this week after last weekend's 2-1 defeat to Roma.
Napoli had won 3-2 in Austria and could have qualified for the knockout stages if they had claimed all three points as Genk failed to beat Liverpool.
But despite dominating for long periods the hosts proved wasteful in front of goal, with the stalemate a missed opportunity.
A clumsy Kalidou Koulibaly foul on South Korean forward Hwang Hee-chan earned the visitors an early penalty with Haaland, 19, slotting in for his seventh European goal this season.
Jose Callejon hit the post with a header and Lorenzo Insigne spurned a series of chances, with Piotr Zielinski and Fabian Ruiz also misfiring in front of goal.
Napoli could thank Lozano who was their best player on the night and latched onto an Insigne cross for the equaliser.
But back after the break, despite changes made by both coaches there was more of the same with Napoli failing to take advantage of Salzburg's loss of momentum.
Lozano went off to a standing ovation and was substituted by Fernando Llorente late with Arkadiusz Milik coming on for Dries Mertens.
Insigne clipped the bar with a long-range effort on 73 minutes, with Llorente also nodding wide just before the final whistle.
Napoli next travel to Liverpool, who they beat 2-0 in Naples in September, but could now have to wait until the final round before sealing their berth at home against Genk in December.