Vinicius, 19, opened the scoring with a 20-yard stunner before Rodrygo, 18, marked his debut by netting after coming off the bench in the LaLiga victory.
Zidane praised the duo for their impact as Madrid moved a point clear atop the LaLiga table.
"I'm glad for them. Many times we forget that they are 18 years old [sic]," the Madrid coach told a news conference, via AS.
"We have seen the emotion they had of scoring in the [Santiago] Bernabeu. I like Rodrygo's goal."
Vinicius' goal was his first for Madrid since February as he made the most of his third LaLiga start of the season.
Zidane said the goal was important for the Brazilian, while he also praised 21-year-old Uruguayan midfielder Federico Valverde.
"I always try to give them confidence because they are very young boys," he said. "We are here for everyone to improve and I'm happy for him [Vinicius] because he needed this goal.
"We will continue now and try to rest well thinking we have a game on Saturday. It has been a good game in everything.
"Fede Valverde has played a great game and I'm glad because he is very young and has an extraordinary future."
Madrid, who face Atletico in the derby on Saturday, have won back-to-back games since their Champions League loss to Paris Saint-Germain last week.
Asked if Madrid had returned, Zidane said: "We are working and believe in what we do.
"Today, we are happy."