The decision clears the way for Tour de France organizers to officially remove Armstrong's name from the record books, erasing his consecutive victories from 1999-2005.
Tour director Christian Prudhomme has said the race would go along with whatever cycling's governing body decides and will have no official winners for those years.
Armstrong's representatives had no immediate comment.
USADA said Armstrong should be banned and stripped of his Tour titles for "the most sophisticated, professionalized and successful doping program that sport has ever seen" within his U.S. Postal Service and Discovery Channel teams. Under the penalties, he loses all his race results since August 1998.
The USADA report said Armstrong and his teams used steroids, the blood booster EPO and blood transfusions. The report included statements from 11 former teammates who testified against Armstrong, including testimony that he pressured them to take banned drugs.
"I was sickened by what I read in the USADA report," McQuaid said, singling out the testimony of former Armstrong teammate and Salt Lake City native David Zabriskie. "The story he told of how he was coerced and to some extent forced into doping is just mind boggling."
Armstrong denies doping, saying he passed hundreds of drug tests. But he chose not to fight USADA in one of the agency's arbitration hearings, arguing the process was biased against him. USADA's report, released earlier this month, was aimed at showing why the agency ordered the sanctions against him.
"At the moment Lance Armstrong hasn't admitted to anything, yet all the evidence is there in this report that he doped," McQuaid said.
Former Armstrong team director Johan Bruyneel is also facing doping charges, but he is challenging the USADA case in arbitration.
On Sunday, Armstrong greeted about 4,300 cyclists at his Livestrong charity's fundraiser bike ride in Texas, telling the crowd he's faced a "very difficult" few weeks.
"I've been better, but I've also been worse," Armstrong, a cancer survivor, told the crowd.
While drug use allegations have followed the 41-year-old Armstrong throughout much of his career, the USADA report seems to have marked a turning point in the saga. Longtime sponsors Nike, Trek Bicycles and Anheuser-Busch dropped Armstrong last week, as did other companies, and he stepped down as chairman of Livestrong, the cancer awareness charity he founded 15 years ago after surviving testicular cancer which spread to his lungs and brain.
Armstrong's astonishing return from life-threatening illness to the summit of cycling offered an inspirational story that transcended the sport. However, his downfall has ended "one of the most sordid chapters in sports history," USADA said in its 200-page report published two weeks ago.
Armstrong has consistently argued that the USADA system was rigged against him, calling the agency's effort a "witch hunt" which pressured witnesses into cooperating.
"It is for Mr. Armstrong to defend himself against such witness statements that he deems to be incorrect. It is not for the UCI to do so," the governing body said in a statement.
If Armstrong's Tour victories are not reassigned there would be a hole in the record books, marking a shift from how organizers treated similar cases in the past.
When Alberto Contador was stripped of his 2010 Tour victory for a doping violation, organizers awarded the title to Andy Schleck. In 2006, Oscar Pereiro was awarded the victory after the doping disqualification of American rider Floyd Landis.
USADA's position is that the Tour titles should not be given to other riders who finished on the podium, such was the level of doping during Armstrong's era.
The agency said 20 of the 21 riders on the podium in the Tour from 1999 through 2005 have been "directly tied to likely doping through admissions, sanctions, public investigations" or other means. It added that of the 45 riders on the podium between 1996 and 2010, 36 were by cyclists "similarly tainted by doping."
The world's most famous cyclist could still face further sports sanctions and legal challenges. Armstrong could lose his 2000 Olympic time-trial bronze medal and may be targeted with civil lawsuits from ex-sponsors or even the U.S. government.
McQuaid said the UCI's board will meet Friday to discuss the Olympic issue and whether to update other race results taking account of Armstrong's disqualifications.
A so-called "Truth and Reconciliation" commission, which could offer a limited amnesty to riders and officials who confessed to doping practices, will also be discussed, UCI legal adviser Philippe Verbiest said.
In total, 26 people including 15 riders testified to USADA that Armstrong and his teams used and trafficked banned substances and routinely used blood transfusions. Among the witnesses were loyal sidekick George Hincapie and admitted dopers Tyler Hamilton and Landis.
USADA's case also implicated Italian sports doctor Michele Ferrari, depicted as the architect of doping programs, and longtime coach and team manager Bruyneel.
Ferrari who has been targeted in an Italian prosecutor's probe and another medical official, Dr. Luis Garcia del Moral, received lifetime bans.
Bruyneel, team doctor Pedro Celaya and trainer Jose "Pepe" Marti opted to take their cases to arbitration with USADA. The agency could call Armstrong as a witness at those hearings.
Bruyneel, a Belgian former Tour de France rider, lost his job last week as manager of the RadioShack-Nissan Trek team which Armstrong helped found to ride for in the 2010 season.