It is a significant blow for the Scot who was expected to start the Tour for the 13th time on Saturday, an occasion he hoped would provide a lap of honour in his final season as a professional cyclist.
It also poses a potential headache for the Scottish Cycling camp who were relying on the Tour to help the 37-year-old reach peak form in time to defend his Commonwealth Games time trial title on July 31 and compete in the road race three days later.
The news that Millar misses out on a Tour spot will likely come as a surprise to many. Only last week he accidently let slip his selection before apologising swiftly for speaking out of turn ahead of the final nine-man squad being revealed publicly. However, after a poor showing in the 2014 British National Road Championships in recent days, team bosses at Garmin-Sharp would appear to have performed a U-turn.
The rider withdrew from the time trial at the midway point on Thursday due to a chest infection. While his condition had improved by the road race on Sunday, he abandoned it after missing the decisive 10-man move.
Millar clearly had an inkling that the death knell was due to sound on his Tour ambitions.
A message he posted on Twitter in the early hours of Monday morning read: "None of my team will answer the phone to me. I under-performed at the nationals. I'm now so scared about losing my Tour spot I can't sleep."
Those fears were realised hours later when Garmin-Sharp announced that Millar would not be included in the team to be led by Andrew Talansky, the surprise winner of the 2014 Criterium du Dauphine last month.
"I'm devastated that the team don't trust me to do the job as I've always done," Millar told The Guardian. "I'm in shock. I don't understand why I'm not selected. The bottom line is that I was selected when they chose the team a week ago and they pulled me because they were worried about my health; that is counterintuitive because they wanted me to race the nationals to prove I was healthy."
Garmin-Sharp sports director Charly Wegelius insisted that selecting the final nine proved "a very difficult task".
"This year we come into the Tour with a team built around Andrew Talansky," said Wegelius. "Had David Millar been healthy, he would have been a phenomenal team member. We would have loved to have him. Unfortunately, as seen over the weekend, David is sick, so we were forced to make a difficult and sad decision."
Jonathan Vaughters, CEO of Garmin-Sharp and Millar's long-time friend, added: "We are very sorry to leave David Millar home due to illness. His experience is unparalleled and his contributions to the sport and our team are undeniable. We wish things were different for David, but as we look ahead to the Tour, we believe we have selected a strong team and we are committed to helping Andrew build on last year's success."
Scottish Cycling promised to rally round the rider and ensure his preparations for Glasgow 2014 remained on course.
Gary Coltman, head of performance at Scottish Cycling, said: "We are really disappointed for David. His last tour, starting in the UK, was going to be special. He was so determined to end his career at the Tour de France on a high. Once he's re-grouped we will work with him to make sure he has the best preparation to make Scotland proud."
Coltman didn't rule out Millar following Sir Bradley Wiggins to compete on the track at the Games. "It would be an interesting one," he said. "Certainly, it's an option in terms of his ability, but I think it would probably compromise his ambitions in the road events. I've already spoken to him about the opportunities that not riding the Tour de France will bring to get to know the time trial course like the back of his hand. We're focusing on the positives."
Millar is due to retire in September following the Vuelta a Espana and, if selected for Great Britain, the World Road Race Championships.
He is not the only rider to be left to twiddle his thumbs between now and the Commonwealth Games.
Alex Dowsett will not be included in the Spanish outfit Movistar's nine-man team for the Tour de France after picking up an infection.
Wiggins learned last week that had no role in Team Sky's ambitions to defend the title of Chris Froome. Peter Kennaugh, winner of the British National Road Race Championships on Sunday, has also missed out on a Team Sky spot.
That leaves a dwindling British contingent comprising Mark Cavendish for Omega Pharma-QuickStep alongside Team Sky's Geraint Thomas and Froome.