With Dani Carvajal and Eder Militao also absent, it meant Real Madrid were without their first choice back four against the reigning Premier League champions, whilst Lucas Vazquez was ruled out with a hamstring issue.
Goals from Kylian Mbappe, Brahim Diaz and a 92nd minute winner from Jude Bellingham secured the win for Real Madrid, though Ancelotti was quick to heap praise on his makeshift defence.
Real Madrid manager Carlo Ancelotti says he expects Antonio Rudiger and David Alaba to be available against Manchester City next week.
Speaking after the win at the Etihad, Ancelotti talked up the possibility of a double defensive boost for the second leg against Man City at the Santiago Bernabeu.
Still, the Champions League holders managed to come from behind twice on Tuesday night to seal an impressive 3-2 win.