Organisers of the capital's bid spoke of their disappointment after being pipped at the post by Leeds, which will host the Grand Depart in 2014.
However, the city's marketing team says its long-term aim was always to host the first of four stages of the classic race in the capital in 2017.
Tour organisers are thought to have awarded the coveted start to the UK in recognition of Bradley Wiggins's achievement in becoming the first British winner this year.
The proposed route would have been a prelude to the peloton moving through England and Wales, and generated an estimated £50 million for the Scottish economy with some £24m for Edinburgh alone.
An EventScotland spokesman said: "It is disappointing that we have been unsuccessful for the 2014 Grand Depart, but it is great news that the tour is returning in 2014 following British cycling success this year.
"Our initial plans had highlighted 2017 as our preferred date and we have had a positive indication from ASO [tour organisers Amaury Sports Organisation] that the year is still a possibility.
"We have developed a great British bid with strong partners, which would deliver significant benefits to the whole country and we will continue our positive dialogue with ASO in the new year and look at our next steps."
Leeds will host the start – which traditionally comprises of individual time trials – on July 5, 2014, before the race heads to London and on to France.
EventScotland's bid had the backing of the Scottish Government, Welsh Assembly, British Cycling, UK Sport and VisitBritain. Tour director Christian Prudhomme visited the capital last year and sent a technical team to view the proposed race routes in September.
Yorkshire received the backing of former world road race champion Mark Cavendish, double Olympic gold medallist Ed Clancy and Brian Robinson, the first Briton to win a stage of the Tour de France in 1958.
Originally, both camps were bidding for 2016/17, but the success of Team Sky and subsequent "Bradley Wiggins effect" leading to the burgeoning popularity of the sport in the UK, saw ASO intimate a desire to bring that date forward.
A Scottish-based bid has been in the planning stages for five years, although subsequently evolved into a British-wide venture with the aim of bringing the tour to within one hour of 50% of the UK population.
There had been concerns raised, however, that an ambitious proposal for four stages to be held on British soil could be off-putting to organisers with two to three days spent outside France more typical for a Grand Depart. To date, only Germany has had four, back in 1987.
The tour last started in Britain in 2007, staged in London and Kent, creating an estimated economic windfall of £90m for the south-east region.
Mr Prudhomme yesterday praised the "outstanding beauty" and challenging terrain of Yorkshire.
He said: "Since the resounding success of the Grand Depart in London in 2007, we were very keen to return to the United Kingdom.
"Bradley Wiggins's historical victory last July and the enormous crowds that followed the cycling events in the streets of London during the Olympic Games encouraged us to go back earlier than we had initially planned."
British Cycling's president, Brian Cookson, said: "Like every other cycling fan, I am thrilled the world's biggest bike race is coming back to this country. I'm sure Yorkshire will give the 2014 Tour de France a welcome which will stand out in the race's rich history."