The Brazilian pair have been left at home as a precaution after Silva took a knock during Saturday's 5-0 home victory over Sochaux in Ligue 1 and Alex suffered a minor thigh pain.
Brazilian Marquinhos and Frenchman Zoumana Camara are expected to start in their place with Frenchman Christophe Jallet also favoured to replace suspended fullback Gregory Van der Wiel.
Italy's midfielder Marco Verratti is also suspended for the Group C winners, who have 13 points from five matches.
Coach Laurent Blanc had already said on Saturday that key striker Zlatan Ibrahimovic was not going to Portugal.
Benfica have seven points in the group and are joint second with Olympiakos Piraeus, with the Greeks hosting bottom side Anderlecht, who have just one point, in their final match.
(Reporting by Gregory Blachier; Editing by Patrick Johnston)