Goalscorer Marek Hamsik admits “this elimination hurts, as we played on level terms with Villarreal.”
The Slovak's diving header had given Napoli the lead at El Madrigal, but Nilmar and Giuseppe Rossi struck twice on the stroke of half-time to secure a 2-1 victory.
“This elimination hurts, as we played on level terms with a great side like Villarreal,” he told Mediaset.
“Unfortunately, the incidents during the game did not help us. In the last 10 minutes of the first half, Villarreal poured forward and found the two goals.”
Some of Walter Mazzarri's choices caused controversy in the Europa League decider, such as leaving Edinson Cavani on the bench.
“Cavani is certainly a player who makes the difference, but we had played well even without him.”
Now Hamsik and Napoli look ahead to Monday's Scudetto showdown with Milan, although he is keeping their ambitions in check.
“It will be a difficult game against Milan. As for our objectives, I'd be more than happy with Champions League qualification.”
See the latest Serie A predictions and betting tips with Eurotips.co.uk