The Portugal international missed the first-leg through suspension, meaning first John Stones and then Fernandinho had to replace him at right-back.
With Kyle Walker still injured, Pep Guardiola was light on options at right-back even heading into the opening fixture.
Elsewhere, the City boss confirmed after Saturday’s win over Leeds that Nathan Ake would need to be assessed after limping off at Elland Road.
Stones also came off at the Eithad against Madrid, meaning City’s defence is looking depleted as things stand.
Kevin De Bruyne, Bernardo Silva and Riyad Mahrez were all rested over the weekend, so could come back into the starting lineup for what promises to be another enthralling meeting between two of Europe’s heavyweights.
Manchester City predicted XI: Ederson; Cancelo, Dias, Laporte, Zinchenko; Rodri, De Bruyne, Silva; Jesus, Foden, Mahrez.