The double Olympic and world champion announced this morning that he would not compete for Team England at the Games due to illness.
The London 2012 icon, who was expected to go for gold in the 5,000 and 10,000 metre races, had been hailed as one of the star turns of the competition.
The 31-year-old athlete said: "I have taken the tough decision to withdraw from the Commonwealth Games.
"The sickness I had two weeks ago was a big setback for me."
Glasgow 2014 chief executive David Grevemberg admitted Farah's absence was a blow.
He said: ''There's no question we're disappointed that Mo Farah announced he would be withdrawing.
"We're very disappointed for Mo.
"We knew how much he wanted to be here.
''I'm sure there will be some disappointed people but there are plenty of great athletes who are here and will be competing.''
Farah had made good progress on his recovery from a recent illness but has chosen to focus on getting back to full fitness in time for next month's European Championships in Zurich.
His withdrawal comes three days after athlete Katarina Johnson-Thompson, new mother Jessica Ennis-Hill's heir apparent, was forced out of the competition by a foot injury.
It means long jumper Greg Rutherford, who has himself withdrawn from his last two competitions for fitness reasons after struggling with a knee problem, is the only member of the golden trio from Super Saturday at London 2012 left in the England team.
Farah, who pulled out of his last two races, had been training hard at his altitude base in Font Romeu in the Pyrenees in a bid to be fit for the Games.
He said: ''Training is getting better here in Font Romeu but I need another few weeks to get back to the level I was at in 2012 and 2013.
''I really wanted to add the Commonwealth titles to my Olympic and World championships but the event is coming a few weeks too soon for me as my body is telling me it's not ready to race yet.
''Best wishes to my fellow athletes in Glasgow.''
Team England chef de mission Jan Paterson said: ''It is a real blow for any athlete to miss out on a major championships through injury, but to have fought so hard to regain full fitness and to have to take such a difficult decision at this stage is particularly hard.
''We wish Mo all the very best and hope to see him back to his peak very soon.''
The news comes hours after Glasgow welcomed the world at a Commonwealth Games ceremony featuring humour, music and a major fundraising appeal.
The spectacle at Celtic Park marked the official start of the 20th Games.
As Commonwealth head the Queen received the ceremonial baton and read out a message of good wishes to the 4,500 athletes and officials taking part.
An audience of around 40,000 and an estimated one billion global viewers watched as competitors from 71 nations and territories paraded on the eve of the competition, with the biggest cheers reserved for Team Scotland.
A cast of 2,000 were involved in the two-and-a-half hour show which acted as a celebration of all things Scottish, from Tunnock's teacakes to the Forth Rail Bridge.
There were poignant moments too, when Scotland's First Minister led a minute silence for the Malaysia Airlines plane victims and there was a tribute to Nelson Mandela from comedian Billy Connolly.
The Queen said: "The baton has arrived here in Glasgow, a city renowned for its dynamic cultural and sporting achievements and for the warmth of its people, for this opening ceremony of the Friendly Games."
Glasgow-born entertainer John Barrowman kicked off proceedings with Karen Dunbar from the comedy sketch show Chewin' The Fat in a quirky tour of Scotland taking in Edinburgh Castle, The Loch Ness Monster and Glasgow's Finnieston Crane.
Barrowman kissed a male cast member at a mock Gretna Green in the colourful show which also celebrated decades of pioneering Scottish inventors.
Glasgow singer Amy Macdonald joined rocker Rod Stewart for a rendition of his hit Rhythm Of My Heart, while Susan Boyle appeared to stumble slightly over the words of Mull Of Kintyre.
There were huge cheers for the parading teams - and the jacketed Scottie dogs which were lead out in front of each group.
The Saltire was held aloft by judo's Euan Burton, who said: "It was a phenomenal reception when we entered the stadium.
"It's a windy evening and the flag is fluttering high.
"I'm so proud to be leading the team."
There was a brief moment of embarrassment when the baton containing the Queen's message refused to open for Prince Imran of Malaysia, the president of the Commonwealth Games Federation.
But Sir Chris Hoy, who was given the honour of delivering the baton to the royal box, came to the rescue.
Sir Chris joined Scottish actors Ewan McGregor, who was on screen, and James McAvoy in an unprecedented appeal for donations to Unicef's Children of the Commonwealth Fund.
The charity said this morning that £3.1 million has already been raised to help young people across the nations.
First Minister Alex Salmond said at the ceremony: "It is Scotland's honour to stage and setting 11 days of celebration of sport and culture which are our Commonwealth Games.
"They belong to us all.
"So from the people of Scotland let us affirm the most important message of all.
"Welcome to the Commonwealth of nations.
"Failte gu Alba.
"Welcome to Scotland."
The event, seven years in the planning, was brought to a close with a spectacular fireworks display at the stadium and across the city.