Keegan had named a largely settled side for the previous eight games, but he lost Geremi, Obafemi Martins and substitute David Edgar in the run up to the final game of the season at Goodison Park.
Geremi returned to Cameroon after a family bereavement, while Obafemi Martins suffered a knee injury in training.
Edgar is expected to have a hernia operation this week after pulling out of the squad on Saturday morning.