Goals from Goran Pandev and Duvan Zapata were not enough to see Napoli through to the quarter-finals as Nabil Ghilas and Ricardo Quaresma plundered two quick goals for Porto, who had won the first leg 1-0.
The Azzurri had piled forward throughout the match at the Stadio San Paolo and might have scored more goals with Dries Mertens and Lorenzo Insigne particularly unlucky in the final third.
Their Spanish coach Benitez thought the 2-2 draw was "extraordinary" but rued his side's failure to enter the pot for Friday's last-eight draw in Nyon.
"I believe that the team have played an extraordinary match, we had control, intensity and speed for at least one hour," he told sscnapoli.it.
"We scored one goal but we should have scored another and closed out the game. Unfortunately we didn't convert, they had a chance and they took advantage.
"However, it was a one-way match."
Pandev beat the offside trap to open the scoring in the 20th minute before substitute Ghilas levelled with a 69th-minute penalty. Quaresma then killed Napoli off with brilliant individual effort, meaning Zapata's stoppage-time goal was mere consolation for the hosts.
Benitez now turns his focus back to Serie A and Sunday evening's meeting with Fiorentina, who also exited the Europa League on Thursday night after being defeated by Juventus.
"We watched a stellar performance and Pandev's qualities are not in doubt," he added. "Up to now we have played more than 40 matches and when I analyse what we have achieved I'm very satisfied.
"As a coach I'm proud of my guys.
"We are third in the league and we are in the Coppa Italia final. In Europe we went out of the Champions League in a stunning way, and (on Thursday night) we should and we could have won.
"For a team in its first year together with a new coach and a new set-up I would say that the overall evolution is looking positive."