Manager Thomas Tuchel has already ruled the Croatian out of Tuesday's tie with a thigh problem, but the Blues have no fresh injury concerns from their narrow win over West Ham United.
Kovacic's absence will see Jorginho and N'Golo Kante continue to man the engine room once more, while Ben Chilwell is sure to keep his place on the left after setting up Timo Werner for the winner at the London Stadium.
Thiago Silva managed to come through the full 90 minutes against West Ham unscathed, so the veteran centre-back should join Azpilicueta and Antonio Rudiger in the back three as Andreas Christensen drops out.
Edouard Mendy has reclaimed his rightful spot in goal over Kepa Arrizabalaga, and he will hope to equal Keylor Navas's record of the fewest goals conceded in his first 10 Champions League matches, having shipped just two goals in nine so far.
Chelsea possible starting lineup:
Mendy; Azpilicueta, Silva, Rudiger; James, Jorginho, Kante, Chilwell; Mount; Werner; Havertz