Greer has been struggling with tonsillitis and did not travel with the rest of Gordon Strachan's squad to Zagreb for the clash with the Group A leaders.
The Scots have already been hit by six withdrawals after Scott Brown, James Forrest, Danny Fox, Lee Wallace, Gary Caldwell and Liam Bridcutt all pulled out.
Grant Hanley went over on his ankle in training earlier in the week, but has declared himself fit.
The Blackburn defender said: "It was just a precaution really. My ankle will be fine and I will be fine."