IOC official said on Thursday after the decision to take away the last major title won by the disgraced American.
The retired Armstrong was stripped of his seven Tour de France titles and banned for life by the International Cycling Union (UCI) in October after several riders testified that he took drugs.
The testimony came in a United States Anti-Doping Agency (USADA) report in which the 41-year-old's former US Postal team was accused of running "the most sophisticated, professionalized and successful doping program that sport has ever seen".
Armstrong, a cancer survivor who founded the Livestrong Foundation, has always denied wrongdoing but is due to appear on US television later on Thursday with reports saying he will confess to taking banned substances.
The 2000 bronze was the only Olympic medal Armstrong ever claimed despite dominating cycling by winning the Tour from 1999 to 2005.
He retired for a second time in 2011.
The IOC had been preparing to make a move for the medal for months but decided at its executive board meeting in December to wait for the UCI to inform the athlete of the titles taken from him and give him the right to appeal.
"Following the recent decisions of USADA and the UCI regarding the competitive cycling results of Lance Armstrong, the IOC has disqualified Armstrong from the events in which he competed at the Sydney 2000 Olympic Games," the IOC said in a statement.
"Namely, the men's individual road race, where he finished 13th, and the men's individual time trial, where he finished 3rd and was awarded with a bronze medal and a certificate."
The IOC has asked Armstrong to return the medal and certificate to the United States Olympic Committee which should send them on to the Olympic ruling body.
"The decision was taken in principle at the IOC Executive Board meeting in December, but its implementation required the expiration of the appeal deadline," the IOC said.
Spaniard Abraham Olano Manzano came fourth in the Sydney time trial and the IOC official said it had yet to be decided if he would be moved up to bronze.
IOC sources said, however, it was very unlikely Manzano would be promoted because the organisation preferred to leave the medal vacant as it has done with the medals of American athlete Marion Jones, also a doping offender, from the same Games.