The winger, who appeared to be targeted by the Manchester United players during Chelsea's FA Cup quarter-final win over the Red Devils on Monday night, didn't travel with the rest of his teammates for the game at the bet365 Stadium today after picking up the issue at Cobham.
It means Willian starts on the left flank for Chelsea, with Pedro on the right flank. With no other major injuries to deal with, Conte starts his usual line-up against Stoke - who Chelsea beat 4-2 in the reverse fixture on New Year's Eve.
Meanwhile, Mark Hughes does not have defender Glen Johnson available today because of a shoulder problem but Marko Arnautovic is back following a bout of illness.
Chelsea starting XI: Courtois; Azpilicueta, David Luiz, Cahill; Moses, Kante, Matic, Alonso; Willian, Diego Costa, Pedro.
Chelsea subs: Begovic, Zouma, Ake, Chalobah, Loftus-Cheek, Fabregas, Batshuayi.
Stoke City starting XI: Grant; Bardsley, Shawcross, M. Indi, Pieters; Ramadan, Cameron, Allen, Arnautovic; Walters, Berahino.
Stoke subs: Given; Muniesa, Whelan, Afellay, Adam, Diouf, Crouch.