The Red Devils defender travelled to the World Cup in South Africa this summer as skipper but saw his tournament ended by a knee injury sustained in the very first training session.
Ferdinand, who has also struggled with back problems recently, has made only one Premier League appearance for the Red Devils this season and is yet to regain his top form.
England boss Fabio Capello handed the captaincy to Steven Gerrard in Ferdinand's absence, with the Liverpool midfielder impressing during the recent qualifying victories over Bulgaria and Switzerland.
Gerrard will again be in his favoured central midfield role for the clash with Montenegro as Frank Lampard continues to work his way back to full fitness following hernia surgery.
Capello must now decide whether to restore Ferdinand to his starting XI, with Everton defender Phil Jagielka having stepped into the breach for the opening two qualifiers.
Former national team captain and Chelsea skipper John Terry is expected to return to the side, but the Italian tactician could elect to keep faith with Jagielka due to Ferdinand's lack of action this term.
Capello will make a decision on his side for the clash at Wembley over the coming days after taking the opportunity to run the rule over his squad in training.