Stones, one of last season's outstanding performers, has been absent since the Community Shield defeat to Arsenal, while Grealish missed the recent England internationals.
Kovacic didn't play in either of Croatia's recent matches, but has featured in all four Premier League games prior to the international break.
"I don’t know (how long for) - I don't think they will be ready for Red Star, but we will see, step by step.
"The injury for Jack is not muscular, but he has an incredible knock on his knee. Still the damage is there.
"John is still a little better, but has a disturbance in his muscles."
And on Kovacic, the boss added he is also out of Saturday's clash.
"It is something muscular, and not a big issue but he’ll be out for tomorrow."