The Brazilian playmaker has been working apart from the rest of the group since Saturday, when he came on as a substitute in Real's 4-2 home win over Getafe in La Liga.
Turkish internationals Nuri Sahin and Hamit Altintop, who have yet to make their debuts since joining Real in the closed season, are also out with knee and back injuries respectively.
German Sami Khedira was included in the squad after recovering from a thigh problem.
The nine-times European Cup winners, who reached the semi-finals last year, play Dinamo on Wednesday. Olympique Lyon and Ajax are the other teams in Group D.
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