Milner scored Newcastle's equaliser in the 1-1 draw at the Stadium of Light earlier in the season and had hoped to make the bench for Sunday's game at St James's Park.
He has been out since the defeat away to Liverpool early last month with a badly bruised foot and the Toon boss says he will not be risked.
Keegan: "James is doing well, but we are going to err on the side of caution and not rush him back and not involve him on Sunday.
"But I fully expect he'll be with us when we go West Ham next weekend."