Kroos was replaced by Luka Modric in the 34th minute at the Santiago Bernabeu while Bale departed in the 83rd minute for James Rodriguez.
Zidane said Kroos will still join up with Germany and Bale with Wales but their fitness will be a concern for their national teams.
Germany play Argentina in a friendly on Wednesday and Estonia in Euro 2020 qualifying four days later.
Ryan Giggs’ Wales face two qualifiers, against Slovakia on Thursday and Croatia the following Sunday.
Real Madrid are yet to confirm the details of their injuries.
“We lost Toni today, we lost Gareth, other players have little problems too,” Zidane said in his post-match press conference.
“But they will travel to play, there is nothing we can do about that. If we could, we would have Toni recover here in Madrid.”
Bale set up Karim Benzema’s opening goal at the Santiago Bernabeu before Eden Hazard and Modric put Madrid three clear.
Granada threatened a comeback when Darwin Machis scored a penalty and Domingos Duarte added a second but James Rodriguez made it four in injury-time to confirm a hard-fought win.
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