Gervinho and Kevin Strootman had put Roma on track for a comfortable victory with first-half goals in the semi-final first leg at the Stadio Olimpico.
An own goal from Morgan De Sanctis and Dries Mertens' strike levelled the contest, but Gervinho popped up to score an 88th-minute winner.
Napoli's comeback delighted Benitez, who was unhappy with their first half but believes they can still win the tie.
"The positive aspect is the reaction of the team, though it was not positive to concede two in the first half," Benitez told Rai Sport.
"The side showed character to fight back and kept positive. Roma had some very fast forwards and it was not easy to defend against them.
"It was tough as the passes were very quick, so hard to defend against."
Napoli were unfortunate to go behind on 13 minutes when Gervinho, who appeared to be in an offside position, got on the end of a Francesco Totti pass to finish.
Strootman scored a superb strike from distance in the 32nd minute before Napoli's fightback started after the break.
De Sanctis palmed the ball into his own net and Mertens finished well on 70 minutes, only for Gervinho to earn Roma the win after a fine team move.
"The third goal was particularly difficult, as we didn't have time to react. The first goal was offside. It was clear, I don't have to say anything," Benitez said.
"We think we can win the second leg and if we do that then we can reach the final. A 1-0 could be sufficient. It's a great shame we conceded the third goal, but our reaction was very, very positive.
"This Napoli is a new team with many new players and to be doing so well is impressive, in my view. I believe we are on the right path to grow."
Benitez described the game as a 'wonderful spectacle', with the second leg to be played in Naples on February 12.
