The club issued a statement on the new ahead of kickoff with United and UEFA accepting the request.
Koke will also miss the game with Jan Oblak set to captain Diego Simeone's hosts.
"Before the start of our Champions League match against Manchester United, a minute's silence will be observed in memory of Ana Merodio Borja, mother of our captain, Koke, who passed away this morning in Madrid.
"Our club requested permission from UEFA to observe a minute's silence both during the first team match and the UEFA Youth League game, as well as for the players to wear black armbands. European football's governing body has granted permission to pay this heartfelt tribute to the mother of our captain and our Juvenil A coach.
"As a sign of respect for her memory, the red and white flag at the Riyadh Air Metropolitano will fly at half-mast."