Acknowledging "a cloud of suspicion would remain hanging over this dark period," the UCI said the list of Tour winners will remain blank for the years from 1999 to 2005.
"This might appear harsh for those who rode clean (but) they would understand there was little honour to be gained in reallocating places," the UCI said after a board meeting in Geneva.
The UCI said Armstrong and "all other affected riders" in the case should return their prize money. That amounts to almost $4 million in Tour money from Armstrong.
Armstrong attorney Sean Breen declined to comment on the prize money demand.
The UCI's decision not to award Armstrong's Tour victories to other riders was welcomed in a statement from the Tour de France's organizers.
"This decision fully coincides with the wishes expressed by the organizers of the race ten days ago," the statement said.
The UCI also ordered an independent outside investigation to examine allegations about the UCI's own conduct and relations with Armstrong raised by the U.S. Anti-Doping Agency report that detailed systematic cheating by the Texan and his teammates.
UCI has been accused of accepting $125,000 from Armstrong to cover up suspicious doping tests.
Riders and officials involved in doping programs will also be targeted by the inquiry commission.
"Part of the independent commission's remit would be to find ways to ensure that persons caught for doping were no longer able to take part in the sport, including as part of an entourage," the UCI said in a statement.
In turn, that move prompted a statement from John Fahey, president of the World Anti-Doping Agency.
"As an independent body itself, WADA supports the decision to set up an independent external commission to examine the problem of doping in cycling," Fahey said.
"The most important thing is for this issue to be dealt with once and for all, and WADA looks forward to the release of further details on the commission's make-up and terms of reference."
A potentially explosive defamation suit filed by the UCI, its president Pat McQuaid and predecessor Hein Verbruggen against Irish journalist and former Tour rider Paul Kimmage has been put on hold, the UCI board said.
Kimmage was scheduled to defend his claims that cycling's leaders protected Armstrong at a Dec. 12 hearing in Vevey, Switzerland. Kimmage has received more than $70,000 in donations from cycling fans to fight his case.
Armstrong's expulsion from the sport he dominated was confirmed Monday when the UCI acknowledged the USADA findings that his teams ran "the most sophisticated, professionalized and successful doping program that sport has ever seen."
Friday's meeting of the UCI board was a necessary legal step to confirm a seven-year hole in the Tour de France roll of honour.
"UCI is determined to turn around this painful episode in the history of our sport," McQuaid said in a statement. "We will take whatever actions are deemed necessary by the independent commission and we will put cycling back on track."
An "independent sports body" will be chosen by UCI within two weeks to nominate members of the advisory panel, which is scheduled to report back by June 2013.
As well as leaving the Tour winner's list blank from 1999-2005, the UCI agreed "not to award victories to any other rider or upgrade other placings in any of the affected events." Other stage-race titles lost by Armstrong include the 2001 Tour of Switzerland and Dauphine Libere in 2002 and '03.
"The (management) committee decided to apply this ruling from now on to any competitive sporting results disqualified due to doping for the period from 1998 to 2005, without prejudice to the statute of limitation," the UCI said.
The UCI did not directly address the status of Armstrong's Olympic time-trial bronze medal from the 2000 Sydney Games, which could be stripped by the International Olympic Committee.
Further revelations of doping are expected in an Italian prosecutor's probe into sports doctor Michele Ferrari, who was identified by USADA as a central figure in the doping programs for Armstrong and the U.S. Postal Service team.
Ferrari was also banned from sport for life by USADA after he chose not to contest its findings at arbitration.
USADA chief executive Travis Tygart has urged the UCI to pursue more doping investigations, and the governing body had talked of seeking to offer limited amnesty in exchange for confessions.
"There are many more details of doping that are hidden, many more doping doctors, and corrupt team directors and the omerta has not yet been fully broken," Tygart said Monday.
Five riders finished second behind Armstrong in his record run of seven straight Tour wins: Alex Zuelle of Switzerland, Jan Ullrich of Germany, Joseba Beloki of Spain, Andreas Kloeden of Germany — later a teammate of Armstrong at Astana and RadioShack — and Ivan Basso of Italy.
Ullrich, the 1997 winner who was denied three more titles by Armstrong, has said he does not want to be upgraded in the standings.
Armstrong is one of three riders stripped of cycling's biggest prize but the only one not to be replaced.
When Alberto Contador lost his 2010 Tour victory for a positive doping test, organizers held a ceremony to award the yellow jersey to Luxembourg's Andy Schleck. In 2006, Oscar Pereiro was awarded the victory after the doping disqualification of American rider Floyd Landis.
Armstrong has not been wiped entirely from cycling's record books. He remains the UCI's world champion in the 1993 road race and winner of the San Sebastian and Walloon Arrow one-day classics in 1995 and 1996, respectively.Suggest a correction