The 37-year-old Scot was expected to be chosen in Garmin's final nine for his 13th and last Tour, before his retirement at the end of the season.
Now Millar has revealed he will not be on the start line in Leeds on Saturday, joining Sir Bradley Wiggins, Pete Kennaugh, Ben Swift (all Team Sky) and Alex Dowsett (Movistar) in missing selection.
Millar wrote on Twitter: "@millarmind: I was selected for TdF last week, then they pulled me last night. Wiggo, Dowsett, Pete, Swifty, fancy a city break? I hear York's nice."
Millar is expected to ride in the Commonwealth Games, where he will defend his road time-trial title.
Like Wiggins, Millar could now also ride on the track as the Tour reaches its climax in the Pyrenees and Paris.