The absence of the 23-year-old 2012 Olympic silver medallist follows checks by the Home Office and Games officials.
The reasons are unclear but Welsh officials have had "rigorous" talks for weeks with "all relevant bodies".
In April the welterweight was ordered to pay a total of £1,228 in fines and costs after admitting his part in a nightclub assault in Birmingham.
The news came on the same afternoon that British 100m champion Dwain Chambers, who was part of England's 4x100m relay team, pulled out of the Games to concentrate on August's European Championships.
Three-time world squash champion Nick Matthew will carry England's flag at Wednesday's opening ceremony in Glasgow, while rhythmic gymnast Frankie Jones will carry the flag for Wales.
Evans' absence is the latest blow for Wales, who have already lost triathletes Helen Jenkins and Non Stanford and cyclist Becky James through injury.
The Welsh have also been seen the expulsion of 800m runner Gareth Warburton, who has been charged with anti-doping rule violations.
And on Monday weightlifter Faye Pittman and judo player Kyle Davies withdrew because of injuries.
Evans, ranked number one in the world in his weight division, was regarded as one of Team Wales' best medal hopes.
Won gold at the Cadet World Championships in Hungary in 2007
Became World Amateur Champion in Baku, Azerbaijan in 2011.
Lost in the welterweight final at London 2012 - beaten by Serik Sapiyev of Kazakhstan
Welsh boxing performance director James Thomas said: "Obviously we were aware of his conviction earlier this year and we certainly don't condone that kind of behaviour but we hoped Fred would have been able to continue to box and improve his lifestyle through the sport."
Wales team boss Brian Davies, who revealed on Monday that in the wake of several big-name withdrawals he was considering rethinking the team's medal target of 27, said everything possible had been done to get Evans to Glasgow.
"The key Welsh and British sporting agencies have been supportive in our attempts to get Fred to the Games and we are bitterly disappointed at the outcome," said Davies.
"Fred is a world-class boxer and has handled this difficult situation in a very disciplined manner - we thank him for his professionalism and wish him all the best for his future ambitions."
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