After Javier Hernandez suffered an ankle injury at Aston Villa on Saturday that is set to rule him out for a month, Ferguson expressed the hope Berbatov would have recovered from his own ankle problem to make the flight to Switzerland.
But the Bulgarian was again absent on Tuesday morning, meaning Ferguson can only count on Wayne Rooney and Danny Welbeck, who has made just one substitute appearance since suffering a muscular problem on England duty last month, in addition to Federico Macheda and Mame Biram Diouf, who have made minimal contributions so far this season.
Rooney is due to face a UEFA appeal hearing in Nyon on Thursday in an attempt to reduce the three-match ban that threatens to rule him out of the entire Euro 2012 group phase.
By then, the 26-year-old will know whether he has any further Champions League action ahead of him this term.
After requiring a last-gasp Ashley Young goal to salvage a point at Old Trafford, United have already encounter difficulties overcoming Basel this term.
And they require at least a point at St Jakob Park on Wednesday evening to claim a place in the last 16.
Ferguson's plans have not been helped by the continued absences of Brazilian twins Rafael and Fabio, in addition to long-term absentees Tom Cleverley and Michael Owen.
Midfielder Michael Carrick is also missing through suspension.
United squad (from): De Gea, Lindegaard, Amos, Evans, Smalling, Vidic, Ferdinand, Evra, Jones, Fryers, Cole, Fletcher, Young, Valencia, Park, Gibson, Nani, Giggs, Macheda, Rooney, Welbeck, Diouf.