The Ruhr valley club will also be missing playmaker Ilkay Guendogan against Werder Bremen on Saturday and possibly against Liverpool in the Europa League next week because his foot injury is taking longer than expected to heal.
Subotic will not be allowed to take part in any form of contact sport for the remaining seven league matches and will undergo individual training.
The 27-year-old, who has dropped down the pecking order and lost his automatic starting spot under coach Thomas Tuchel, is likely to leave at the end of the season.
He will be replaced by Under-23 player Jon Stankovic, Tuchel said,
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Germany international Guendogan has been sidelined for four weeks since picking up the injury in the game against Bayern Munich.
"We do not know why it is taking so long," Tuchel said. "It does not hurt when sprinting or wearing football shoes so we hope he can resume training next week."
Borussia are second in the Bundesliga, five points behind leaders Bayern Munich with seven matches left to play.
They are through to the German Cup last four and the Europa League quarter-finals where they will face former coach Juergen Klopp's Liverpool.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
