The IOC also said that Qatari sprinter Samuel Adelebari Francis had also failed a re-test and had been disqualified from the men's 100 metres in which he finished 16th.
Barrios and Francis were among 98 athletes who have tested positive in reanalysis of samples from both the 2008 Beijing Games and the 2012 London Olympics.
The IOC ordered samples from the two Games to be re-tested using new techniques not available at the time of the competitions in attempt to root out cheating.
Six athletes, including three Russian medallists, were disqualified on Wednesday from their events at the Beijing Games.
Barrios tested positive for the prohibited substance, acetazolamide, a diuretic and masking agent, the IOC said.
It said that the 33-year-old "has the silver medal, the diploma, and the medallist pin obtained in the discus throw event withdrawn and is ordered to return these".
It also added the governing body of athletics, the IAAF, to modify the results of the event and "to consider any further action within its own competence".
Francis tested positive for the banned substance stanozolol, the IOC said. He was also entered for the 200 metres but did not start.
(Writing by Brian Homewood; Editing by Alison Williams)
