Ferdinand has missed United’s recent games against Tottenham and Arsenal with a hamstring injury, but returned against Bolton three days ago.
Nemanja Vidic, Tom Cleverley, Danny Welbeck and Rafael also misses the trip to Lisbon due to injuries.
United boss Sir Alex Ferguson also had no space for strikers Federico Macheda and Mame Biram Diouf in his squad.
Full Manchester United squad: De Gea, Lindegaard; Evans, Evra, Fabio, Jones, Smalling; Anderson, Carrick, Fletcher, Giggs, Nani, Park, Valencia, Young; Berbatov, Hernandez, Owen, Rooney.