On a rainy afternoon at the Bernabeu, an early brace from Cristiano Ronaldo looked to have put them on the path to a comfortable win, but Carlos Comona grabbed one back for the visitors before the break.
Gijon continued to push and despite Real themselves having chances, Abelardo Fernandez's men should have earned a point, with Duje Cop missing a penalty.
However, Los Blancos held on for the victory and, speaking afterwards, Zidane admitted he was less than impressed by his side's lacklustre display.
"It was a difficult game, in which the only good thing was the three points," the coach said after the match. "It's a game for us to forget because things didn't go as we wanted them to, but it is what it is.
"We were lacking a bit in everything, but we're happy for the three points, they’re important.
"The rain? Both teams had to play through it. I have no explanation for why we lacked a bit of everything."