Los Blancos scored twice in the closing stages of the last-16 first-leg tie against the Segunda Division side to make the scoreline look more respectable, having taken the lead through a Gareth Bale penalty.
Bale was the star name in Madrid's starting lineup, which also included Dani Carvajal among the first-team regulars, and Zidane admits that he intends to get the Welshman back up to full speed as soon as possible following a stop-start campaign to date.
"It was important to see how he felt. In the end he played an hour, without problems, feeling physically well," he told reporters. "So we will continue like this. We want him to play regularly now.
"This was not an easy place to come, they have been playing well. They made it tough for us, but we got a good result. Many of these are players who do not play so often. And they did very well, against a team who did not give up.
"I am happy for the players who played a serious game and achieved something good. The tie is never over, we must play another serious game in the second leg. In the second half we had some problems, above all when they were down to 10. But in general I am happy."
Madrid welcome Numancia to the Bernabeu next Wednesday for the return fixture, three days after a trip to Celta Vigo on their return to La Liga action.