The decision by the International Olympic Committee's executive committee came two years after Cox admitted to doping between 2001 and 2004.
The panel said it would be up to the track and field governing body to decide whether to take back the gold medals awarded Cox's teammates.
Cox only competed in the second heat of the 1,600 meters in Athens.
In a January 2010 letter provided to the IOC by the U.S. Anti-Doping Agency, Cox admitted using banned substances. She accepted a four-year suspension and the disqualification of her results, including the Olympics.
Also Saturday, the committee announced the United States' gold medal in the men's 1,600-meter relay from the 2000 Olympics in Sydney would be rescinded because of Antonio Pettigrew's involvement in the BALCO doping scandal. The gold medal was given to Nigeria instead. Jamaica and the Bahamas, which had finished third and fourth, were moved up to silver and bronze medals.