The league leaders said the Dutchman had a "fever" in a statement, while coach Hansi Flick explained Monday that Uruguayan centre-back Ronald Araujo would miss the game because of a "private situation".
Araujo was sent off in Barcelona's 3-0 Champions League defeat by Chelsea last week and Spanish media have reported he has asked for a "mental health break".
"Ronald is not ready at the moment," Flick told reporters Monday. "It's a private situation. I don't want to say more. Please also respect it."
Both De Jong and Araujo missed Saturday's league win over Alaves, the former because of a family issue, and the latter with a stomach bug, Barcelona had said.
The Catalans are also without Fermin Lopez as well as long-term absentees Marc-Andre ter Stegen and Gavi.
Reigning champions Barca are three points clear of Atletico, fourth, before the teams meet at Camp Nou.