Ferdinand picked up a hamstring injury in the club's opening Barclays Premier League fixture against West Brom, and missed subsequent games against Tottenham and Arsenal.
And while the England international did return to play the full 90 minutes against Bolton on Saturday, United have confirmed he is not part of the squad that left for Portugal on Tuesday.
With reports suggesting that Ferdinand pulled up fine from the weekend's encounter at the Reebok Stadium, it is likely that he has been omitted from the United travelling squad as a precautionary measure, especially with the club due to play a vital league encounter against Chelsea on Sunday.
Ferdinand's regular partner in central defence Nemanja Vidic will also not be available against Benfica, along with Tom Cleverley, Danny Welbeck and Rafael.
However, United received good news in the form of Patrice Evra and Jonny Evans, who were both on the plane to Portugal despite having picked up knocks against Bolton.
Man United squad: David de Gea, Anders Lindegaard, Jonny Evans, Patrice Evra, Fabio, Phil Jones, Chris Smalling, Anderson, Michael Carrick, Darren Fletcher, Ryan Giggs, Nani, Park Ji-sung, Antonio Valencia, Ashley Young, Dimitar Berbatov, Javier Hernandez, Michael Owen, Wayne Rooney.