The French international headed home in the 20th minute to make it 1-1 after Lorenzo Insigne had put the Neapolitans ahead.
Second-half strikes from Toni Kroos and Casemiro ensured a handy first leg advantage for Los Blancos.
"Benzema has a lot of personality, and he showed that he knows how best to respond in critical moments," the Real boss stated in his post-match comments.
"He deserved to score, and was a constant danger."
The former Lyon star's goal canceled out an Insigne strike that Zidane felt came against the run of play.
"It's annoying to have conceded early considering how well we played right from the start, but I'm glad that we were able to respond quickly," he said.
The 44-year-old also addressed the performance of James Rodriguez, who has been regularly linked with a move away from the club having struggled for playing time this season.
"[Rodriguez] is a Real Madrid player. Everyone is always ready to play at this club," the tactician pointed out.
"He gave us peace of mind on the ball in the first half, and I'm very happy with his performance and that of the whole team," he added.
One of the novelties of the match was the rare sight of captain Sergio Ramos being substituted, and the Andalusian's former teammate and now coach was happy to outline his reasons.
"[Sergio] Ramos had a knock from the beginning and also picked up a yellow card," he explained.
Finally, the French boss echoed midfielder Casemiro's comments in highlighting the work that remains to be done if Los Blancos are to qualify for the quarter-finals.
"The round is not over yet," he concluded. "We have to go to Naples and be prepared to fight and suffer if we want to go through."
Real Madrid equal their best-ever scoring streak
Once Karim Benzema had equalized for Real Madrid against Napoli, it meant Los Blancos had equalized their all-time record of scoring in 41 consecutive matches.
It's the fourth time that the club has achieved the mark in its 115 years of existence.
The last game in which Real did not find the net was against Manchester City in the Champions League semi-final on April 26, 2016.
On that occasion, the game ended goalless.
Real Sociedad were next up, on matchday 36 of the 2015/16 LaLiga season and since then, 110 goals have been rifled home in those 41 games.
Jose Mourinho was on the bench in the 2011/12 campaign, the last time the club reached the mark, and during that period the team scored a monumental 135 goals and eventually went on to win LaLiga.
In 87/88 and 88/89, when Leo Beenhakker was at the helm, Real scored 103 goals and secured a league and cup double.
The first time the record was achieved was in the 51/52 and 52/53 seasons.
Ipina presided over a team including top scorer Pahino, with 35 goals, Roque Olsen, who got 17, and Luis Molowny, with 11.
Barcelona hold the absolute record in Spain, scoring in 44 consecutive games between the 1942/43 and 1943/44.
Maradona delivers pre-match talk to Napoli players
If Napoli needed any more motivation to beat Real Madrid at the Estadio Santiago Bernabeu, it came in the form of Diego Maradona, who arrived in the dressing room pre-match to deliver a teamtalk to the players from his ex-club.
He wasn't going to pass up the opportunity before taking his seat, to give the visitors his pearls of wisdom, and it came at the end of an interesting day.
It started with a Police investigation concerning a domestic violence complaint, and then during the afternoon, Maradona walked out of the official board of directors dinner.
Reina: A warm San Paolo reception awaits Real Madrid
Napoli goalkeeper Pepe Reina admits Real Madrid were far superior during their 3-1 defeat at the Estadio Santiago Bernabeu and caused numerous problems for the away side.
Lorenzo Insigne initially shocked Los Blancos, giving Napoli an eight minute lead, but Karim Benzema, Toni Kroos, and a wonderful Casemiro volley sealed defeat for the visitors.
"It's a result that hurts us, it's a fair result because they created a lot of problems of us," Reina told reporters.
"They made us defend very deep and we were uncomfortable because we had a lot of space ahead of us."
However, with an away goal under their belt, Reina believes a 2-0 win at the Stadio San Paolo in three weeks' time is achievable, and it's an objective the team have set themselves.
"We can win 2-0 at home and it's the challenge that will set us out to do," the Napoli man said. "The away goal is important and we're going to have to be tight from the start.
"A warm San Paolo reception awaits."
No excuses for Wenger as pressure mounts
Arsenal manager Arsene Wenger was not looking for excuses after his team were demolished 5-1 by Bayern Munich in their Champions League round of 16 first-leg game on Wednesday.
Arsenal look certain to exit Europe's premier club competition at the first knockout stage for the seventh season in a row and the pressure on Wenger is mounting.
"I don't look for excuses," the Frenchman told reporters.
"It's a shock of course to lose at that level. We made everything wrong, the fifth goal shows that."
Wenger has been Arsenal manager since 1996 but they have not won the Premier League title since 2004 and, 10 points behind leaders Chelsea, look very unlikely to achieve the feat this season.
"These kind of games you need to be focused on for 90 minutes. I felt the third goal was a killer for our players and after that we had no response," Wenger said.
Wenger was asked if this result was his lowest point as a manager.
"How I feel I don't think is the most important (thing) but of course it is disappointing," he said.
Former Arsenal players led the calls for Wenger to be replaced.
"He looked particularly wounded. I feel for him - he almost needs to be protected from himself," Martin Keown, a member of Wenger's squad who went through the 2003-04 Premier League campaign unbeaten, told BT Sport.
"This is 20 years of work here. He's been magnificent for the club. This is a massive low point for him. This brings forward the change that looks likely at the end of the season," the former England defender added.
"I think it will be him that makes the decision. The realisation that the decision needs to be made is more apparent tonight."
Arsenal recovered from conceding an early goal to equalize and the game was poised at 1-1 at halftime before the Premier League club's key defender Laurent Koscielny was forced off through injury early in the second half.
"It's difficult to explain. I felt we had two good chances to score just before halftime," Wenger said.
"I felt we were unlucky for the second goal, the referee gave a corner for us at first. Then we concede the second goal and then ... we lost Koscielny. We collapsed."
Neymar: Barcelona have 1 percent chance of qualifying
Barcelona forward Neymar has confessed that while his side believes they can overturn their Champions League deficit, there is only a one percent chance of them reaching the quarter-finals.
Luis Enrique's men were on the receiving end of a 4-0 thrashing at the hands of Paris Saint-Germain on Tuesday night, leaving their expectations of progression in tatters.
"While there is a 1 percent chance, we have 99 percent faith," the Brazilian wrote on Instagram.