The Italian made his first appearance in the Blues' 2-1 win over Leicester City on Saturday although is selected from the start at Stamford Bridge on Tuesday night.
Chelsea team: Courtois; Azpilicueta, Christensen, Cahill (c); Zappacosta, Kante, Fabregas, Alonso; Willian, Batshuayi, Pedro. #CHEQAR— Chelsea FC (@ChelseaFC) September 12, 2017
Batshuayi, who hasn't started since the Premier League defeat to Burnley on the opening weekend of the season, also features in the XI, replacing the in-form Alvaro Morata.
As confirmed by Antonio Conte in Monday's press conference, Eden Hazard remains on the bench as he continues to work his way back to full fitness following an ankle injury.
David Luiz, perhaps surprisingly, is another to be absent from the starting XI, with summer signing from Monaco Tiemoue Bakayoko also named as a substitute.
Chelsea starting XI: Courtois, Azpilicueta, Christensen, Cahill, Zappacosta, Kante, Fabregas, Alonso,Willian, Batshuayi, Pedro.
Chelsea subs: Caballero, Rudiger, David Luiz, Moses, Bakayoko, Hazard, Morata.
Qarabag starting XI: Sehic, Medvedev, Sadiqov, Huseynov, Jeznicak, Qarayev, Almeyda, Gerrye, Micel, Enrike, Ndlovu.
Qarabag subs: Kanibolotskiy, Amirgliyev, Madatov, Elyounoussi, Ismayilov, Yunuszada, Diniyev.