Jose Callejon's 81st-minute header was all the hosts needed at the Stadio San Paolo, moving to within three points of second-placed Roma in the Serie A.
Having lost Valon Behrami (knee) and Jorginho (flu) pre-match, Benitez praised his side for still having the character to claim three points.
"We've seen many games that Napoli played well and didn't win, so to beat a strong side like Roma I think we ought to be happy," Benitez told Sky Sport Italia.
"I think we are the only team this season who have beaten Roma twice. That must mean we are doing something right.
"We lost Valon Behrami and Jorginho this morning, so had to change things around, which made the win even more pleasing.
"We had quality throughout the year and without certain players today we still had intensity, scoring opportunities and kept a clean sheet."
Faouzi Ghoulam picked out Callejon at the back post and the attacker found the top corner with his header, which went in off the post for the game's only goal.
Benitez was unhappy with how often his team turned over possession, but was pleased his side took their chance.
"Of course we had a few problems on the counter-attack, but that was because we lost the ball, so we have to work on that," he said.
"Our idea is to attack and we went forward from the start trying to get the victory.
"I think both teams had their chances and it could've gone either way, but we took our opportunity and won the game."
Benitez also defended midfielder Marek Hamsik as the Slovakian continues to struggle on his return from injury.
"At the start of the season he did very well, but he was out for two months and is really struggling to regain full fitness," the Spaniard said.
"We know he has the quality and will get there eventually."
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