BVB's Germany international admits he may not be fit in time for the Bundesliga champions' clash against Los Blancos
Both were also unavailable for Saturday's domestic derby against Schalke a game in which they lost further ground on the leaders, Bayern Munich, after the 2-1 defeat.
And Gundogan revealed he is not getting his hopes about making the clash with Los Blancos.
"As things stand, I do not expect to be fit for Wednesday," Gundogan told reporters.
Left-back Marcel Schmelzer has a bruised foot, and also remains a doubt for Jurgen Klopp's side but Mario Gotze who missed the Revierderby could be in a contention for a start against La Liga giants.
BVB has four points in the Group D standings and are two points behind Madrid.