Bale was substituted during the second half of last week's 2-1 victory over the Bundesliga champions at the Allianz Arena and sat out the 3-2 win at Sporting Gijon in LaLiga on Saturday.
The Wales forward was sidelined for three months due to ankle tendon surgery this season and was also laid low by calf issues last term.
As such, Zidane is not willing to take any unnecessary risks with the 27-year-old.
"Gareth has been working hard to get back and to play with the side and, after his three months out from injury, he's come back and was very excited about playing again," the Frenchman told a pre-match news conference.
"But he's got a little problem that has come up again. We hope it's nothing.
"In a few more days he should be back with us. Tomorrow [Tuesday] he will not be ready. We don't want to risk anything with him but he should be ready in a few days.
"He's keen to get back as quick as possible and be with us, so we'll see from now until the end of the season."
Madrid have entered a pivotal week in their season, hosting bitter rivals Barcelona - who they hold a three-point advantage over and have played one game fewer than - in what could prove to be LaLiga's title decider on Sunday.
"I don't know, I hope so," Zidane said when asked whether Bale would be back for El Clasico.
"I hope he can be with us. I can't assure you of anything, I can't tell you anything."
Isco produced a virtuoso display in Gijon, his last-minute winner the second of two brilliant goals.
It was an impressive audition to take Bale's place from a player who has been restricted to just 77 minutes of Champions League football by Zidane's squad rotation system this season.
Nevertheless, the Madrid boss was determined to give very little away.
"It could be Isco, it could be any of them. They're all ready to play and that's the most important thing for me," he said.
"I've decided but the problem is I can't tell you. You said it in your question, everyone is playing well.
"I have to make a choice and I'm happy that they are all playing to a very high level to make it difficult for me."
On Isco's sparing use in the Champions League, Zidane added: "There's no explanation. With squad rotation, with playing with other players, these are things that happen
"It's just a coincidence. When you look at the statistics, it's true. It must be tough for him to have only played 77 minutes in the Champions league but we've got a lot of important games and we'll see what's going to happen tomorrow."
While Zidane must do without one of his star attackers, Bayern are set to benefit from the return of Robert Lewandowski after their top scorer sat out the first leg with a shoulder complaint.
"You know how good he is. He's an authentic number nine and a great player for Bayern," Zidane said.
"I'm not worried. I know the side they have and know they're good all over the pitch. We have to be ready, focused and work on what we have to do."