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Algerian international Adam Ounas had put Napoli ahead after 52 minutes at a sparsely-attended San Paolo Stadium only for Ralph Hasenhuettl’s side to battle back with three late goals in the last 32, first leg tie.
German international Werner equalised after 61 minutes with Portuguese winger Bruma pulling the Bundesliga second-placed team ahead on 74 minutes. Werner then added his second three minutes into injury time.
“It’s a pity, because with 2-1 we still could have turned it around, but needing a 3-0 win in Germany it now becomes very difficult,” said Napoli captain Marek Hamsik.
“Conceding three goals at home in Europe over 90 minutes is not good, but it’s not the Napoli we usually see.”
He added: “It’s also different playing in front of 40,000 compared to 15,000, especially when so many of them were German fans. It still shouldn’t affect us, as we are in a European tournament.”
Maurizio Sarri’s side had dropped down into the second-tier European competition after their Champions League exit with the tie generating little interest in the southern Italian city where the dream this season is to win their first Scudetto since the glory days of Diego Maradona back in 1990.
Maradona had also led the team to their only success in the tournament’s predecessor, the UEFA Cup in 1988.
Sarri left out some of his big names ahead of Serie A action this weekend with Belgian Dries Mertens suspended and regulars like Lorenzo Insigne and midfielders Allan and Jorginho not starting.
The absense of their stars allowed the Germans, who had almost as much support in the crowd as the Italians, space with Werner pushing forward early but his effort was held by by Pepe Reina.
Leipzig also had chances through Bruma and Yussuf Poulsen before Napoli’s Jose Callejon failed to make the most of a defensive error by the Germans allowing Hungarian goalkeeper Peter Gulacsi to clear.
Marko Rog set up the opener early in the second half when he picked up the ball outside the box, crossing for Ounas, who finished off with a low angled drive.
Leipzig tried to react with Poulsen testing Reina who parried from close range, before Werner found a way through.
Substitute Lorenzo Insigne had a chance to pull Napoli ahead again off a Callejon cross but Gulasci made a save.
Bruma then tapped in the second for the Germans helped by Christian Maggio, with Werner grabbing the third in a frenzied finish for both sides.
“It’s disappointing that my first goal in a Napoli jersey coincided with a defeat, as it became meaningless,” said Ounas.
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