The London club will qualify for the last 16 of the competition if they win in Ukraine but manager Arsene Wenger can ill afford to lose Fabregas who has just returned from a month on the sidelines.
"Cesc will not travel," Wenger told Arsenal's website.
"It's a mixture of caution and his hamstring. We cannot take the gamble. He has a good chance to play (against Newcastle) on Sunday but tomorrow would be a risk."
Alex Song is also doubtful for the Group H clash with a calf strain, as are Andrei Arshavin and Denilson who have groin injuries.
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