The trio all missed the 2-2 draw at Cardiff City on Sunday but could be available for the Champions League tie as manager David Moyes ponders his selection options.
Rafael has been out since hurting his ankle during the 3-1 win against Fulham while Vidic suffered concussion against Arsenal. Jones was injured whilst on international duty with England.
Marouane Fellaini (suspended) and Darren Fletcher (ineligible) were also involved in the session but will not play at the BayArena.
Manager Moyes will hold a press conference on Tuesday ahead of a real test against a side that sits second in the Bundesliga. United lead Group A, one point clear of the BayArena outfit, with Shakhtar Donetsk a further two points adrift in third place.