Benzema scored eight Madrid goals in a row before suffering an injury and Los Blancos had failed to score in their previous two matches. But, despite being without the Frenchman, there was no space for Gareth Bale in the squad.
Zidane reserved special praise for Brahim following his performance at the Bernabeu.
"Brahim is a player who goes straight for goal when he gets the ball," Zidane said. "He always wants to look for space.
"The first goal was his pressure, we won the ball back and scored. Happy with his performance and with the victory which the players needed."
However, he was less forthcoming when asked what Bale's omission meant for the Wales international's future in the Spanish capital.
"I am the coach, up to me to pick the squad," he added. "You can interpret it as you want.
"I have to make a list of players, and some players will always have to miss out."
Madrid were pegged back on 11 minutes when Gerard Moreno robbed Casemiro before unleashing a stunning effort by Thibaut Courtois. Madrid took the lead again five minutes before half-time when Marcelo's effort bobbled into the path of Jesus Vallejo, who tapped into an empty net.
Villarreal pulled a second goal back in stoppage time through Jaume Costa.
One of the main high points for Zidane will have been Brahim's performance. The former Manchester City man was given a standing ovation by the Bernabeu when he was came off on 74 minutes.
In his place, Madrid welcomed back Vinicius Junior, who had not played since injuring himself during the 4-1 defeat to Ajax in the Champions League round of 16.
Victory means Madrid could still finish second should they win their remaining three matches and Atletico lose theirs.
Meanwhile, Villarreal are still not safe as 18th-place Valladolid are five points behind them with three match remaining.