Benzema’s spectacular 89th-minute strike made it two wins from two since Zidane returned to the club earlier this month.
However, Real were far from their best at the Santiago Bernabeu against a side seven points adrift of safety at the bottom of the table with just five league wins this season.
Juan Camilo Hernandez gave Huesca a shock early lead before Isco and Dani Ceballos put Los Blancos in front midway through the second half.
But Xabier Etxeita levelled for Huesca with 14 minutes left and they looked on course for a memorable point before Benzema’s late intervention.
Speaking to reporters after the game Zidane defended his team’s performance, conceding it is hard to get the maximum out of his players given they have little to play for this season.
“Obviously, we can play much better than we did today. But I’m happy for the victory and the efforts. Huesca deserved more than a defeat,” said Zidane.
“The changes? I tried to build the best possible team to win, and today it was important to make changes after the international break.
“Anyway, it’s impossible to win a title nowadays with just 13 players in your squad. And to make it clear: I’m not trying to keep everybody happy.
“It’s hard to motivate the team when you know you are not going to win any title this season.”
Zidane sprung a surprise before kick-off by selecting his son Luca, to make just his first appearance for the club since the final game of last season.
Zidane defended his selection after the game, revealing that Thibaut Courtois was injured and Keylor Navas was rested.
“I’m happy for Luca’s first victory with Real Madrid,” he added. “Courtois wasn’t fine, and I wanted to give some rest to Keylor. I think everything was all right”.