The midfielder linked up with Steve Clarke's side for November's fixtures but missed Friday night's 2-0 success over Moldova due to a throat infection.
McTominay was already classed as a doubt for the dead rubber with Denmark on Monday, but Clarke has now confirmed that the 24-year-old will not make the cut.
Speaking to reporters at a press conference, the Scotland boss said: "Scott is definitely out. Scott hasn't recovered enough from his virus."
With McTominay playing a key role under Ole Gunnar Solskjaer this term, the Red Devils will hope to have him back for Saturday's Premier League encounter with Watford.
The Scotland international has made 12 appearances in all competitions for United this season but is still waiting for his first goal contribution of the campaign. body check tags ::