Mariano Diaz scored a pair of goals and Jesus Vallejo added another as Madrid won a largely inconsequential match at the Santiago Bernabeu.
Bale's omission was notable, however, with the Wales star's future at Madrid in doubt beyond this season.
Zidane gave Bale the start on Wednesday but the 29-year-old failed to impress as the Blancos fell to a shock 1-0 defeat to Rayo Vallecano.
Bale was not even on the bench in Madrid's next match, and Zidane would not elaborate on the Welshman's absence following Sunday's game.
"I'm the coach and I have to make a list. Nothing else," Zidane said in his press conference.
"It is not a message. You can interpret what you want. I have to make a list of players, and someone has to stay out."
Bale has been regularly linked with a summer exit from Madrid, with a return to the Premier League considered the most likely option.
Though Bale’s agent has looked to quell the exit rumours, Sunday's omission appears to be another sign that Bale's long-term future at the Bernabeu is in doubt.
Diaz is another player whose future at Madrid appears to be in question, with the striker failing to make an impact in his first season back at Madrid after a summer move from Lyon.
Form and fitness have hampered Diaz, who came up through the Madrid academy before signing with Lyon in 2017.
The 25-year-old's double on Sunday took him to just three league goals for the season, and Zidane was happy for a player who has struggled to break through in 2018-19.
"Of course he has not had many opportunities, because he was injured for a long time," Zidane said of Diaz.
"But Mariano today had the opportunity to play, he scored two and I'm happy for him."