If United qualify from the group stages - the club's last Group C game is at home to Valencia on 7 December - they can then name a new squad of players for the knockout stages.
Bebe's exclusion from United's initial Champions League squad would have raised eyebrows as he only joined in August from Vitoria de Guimaraes at a cost of over £7m.
Hargreaves underwent knee surgery in the United States in 2008 in a bid to solve his long-term tendinitis problem.
United boss Sir Alex Ferguson has said the England midfielder "continues to battle for full fitness", but Hargreaves' exclusion from the Champions League squad suggests the manager does not expect him to make a full return much before Christmas.
The former Bayern Munich player, who joined Manchester United in 2007 in a £17m deal, played several reserve matches towards the end of last season and came on as a late substitute in United's 1-0 win over Sunderland in the penultimate game of the season on 2 May.
But the Canadian-born midfielder was hit by an injury setback in July and returned to the US to see a specialist over the injury.
Under new rules introduced this season all clubs in the Premier League must submit a squad with a maximum of 25 players and containing eight home-grown players.
And the duo's selection in the latter was arguably a formality as all senior players at the club - excluding those out on loan - were registered.
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