"I can announce that we have communicated to Tyler Hamilton that he has been disqualified and we will reallocate the medals," IOC spokesman Mark Adams told reporters after a disciplinary commission meeting in London.
The IOC was eager to close the case before the end of the eight-year statute of limitation but had waited for information from the U.S. Anti-Doping Agency in case there was involvement of other riders or coaches in that race.
Retired Russian rider Viatcheslav Ekimov will be awarded Hamilton's gold medal with American Bobby Julich upgraded to silver and Michael Rogers of Australia moving up from fourth to bronze.
Hamilton was initially allowed to keep his medal in 2004, after testing positive for blood doping, because the laboratory accidentally destroyed his B sample by deep-freezing it.
The following year, Hamilton tested positive for a blood transfusion and was banned for two years.
In 2006 he was linked to the Spanish doping scandal dubbed "Operation Puerto" before testing positive for steroids three years later. He was given an eight-year ban after he said he had taken an over-the-counter treatment for depression.
In an interview last year Hamilton ended years of denials by admitting he had used performance-enhancing drugs.