Andreas Christensen is missing from the Chelsea squad for the second leg of the last-16 tie so Zouma comes in alongside Cesar Azpilicueta and Antonio Rudiger in the back three.
Olivier Giroud is on the bench and Kai Havertz will continue as a false nine.
Chelsea manager Thomas Tuchel makes five changes to the side that drew 0-0 against Leeds at the weekend.
There is no place in the starting line-up for Christian Pulisic or Callum Hudson-Odoi, who are both on the bench.
Reece James and Marcos Alonso start as the two full-backs.
Chelsea, who are defending a 1-0 lead from the first leg, are without suspended duo Mason Mount and Jorginho, as well as the injured Thiago Silva and Tammy Abraham.
Chelsea XI: Mendy; Azpilicueta, Zouma, Rudiger; James, Kante, Kovacic, Alonso; Ziyech, Havertz; Werner.
Subs: Kepa, Caballero, Emerson, Anjorin, Chilwell, Hudson-Odoi, Gilmour, Pulisic, Giroud.
Atletico XI: Oblak; Trippier, Savic, Gimenez, Lodl; Llorente, Koke, Saul, Carrasco; Luis Suarez, Joao Felix
Subs: Grbic, San Roman, Kondogbia, Torreira, Correa, Lemar, Herrera, Felipe, Dembele, Vitolo, Hermoso, Vrsaljko.