He was originally named in Carlo Ancelotti’s starting XI for the game at the Etihad on New Year’s Day.
Bernard looked to be complaining of a knee injury as he received treatment during the warm-up.
It was decided he could not play in the match and Tom Davies was promoted to the team in his place.
Carlo Ancelotti also made four changes to his Everton side that beat Newcastle 2-1 with Yerry Mina, Lucas Digne, Seamus Coleman and Fabian Delph coming in.
Manchester City were again without goalkeeper Ederson as they hosted the Toffees at the Etihad Stadium.
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