The France international ended a run of six games without a goal when he headed in Dani Carvajal's cross to cancel out Lorenzo Insigne's opener at the Santiago Bernabeu.
Further strikes from Toni Kroos and Casemiro secured the win for Madrid that gives them a solid advantage heading into the second leg of their last-16 encounter.
Zidane was frustrated with the fact that Insigne's opening goal came after a strong start from his own side but credited Benzema for rising to the occasion to help them get a foothold in the match.
"That's the way football is. It's a pain that, playing as we did from the start, with that intensity, they go and score. It's a bit f***** up," said Zidane.
"But in the end, we scored straight away and we got into the game.
"Benzema showed that he has personality and that, in critical moments, he knows how to answer in the best way possible - by scoring. I would have liked him to get one more because he had chances. When he moves in that way, he's a constant danger."
Zidane warned his players that the tie is far from over, however, with Napoli knowing that a 2-0 win at the San Paolo will be good enough to send them through.
"It's still 50-50," he said. "It'll be a second leg and they will make it difficult. I would have liked not to concede. It's a good result, but it's not decisive. It's not enough to settle the tie."
Zidane handed a surprise start to James Rodriguez and the former France star was delighted with the attacking midfielder's contribution.
"James is our player and that's why I put him in," he said. "He did very well. He helped keep us calm with his play on the ball, especially in the first half. And he's very good with crosses. I'm happy for his game, as I am with everyone's."
There were some concerns when captain Sergio Ramos was substituted midway through the second half, but Zidane explained that he was keen both to avoid aggravating a minor injury and ensure that the centre-back did not collect a second yellow card.
"Ramos had a knock from the start and then I took him off because of the yellow," he added.