Park had begged for a chance to compete in what would be his third, and almost certainly last, Olympics - at one point getting down on his hands and knees during a media conference.
The 26-year-old was once the poster-boy of South Korean swimming, courted by advertisers and idolized by fans.
He won 400m freestyle gold and 200m freestyle silver at the 2008 Beijing Olympics, and two silver medals at the 2012 London Olympics as well as 400m world titles in 2007 and 2011.
In his competitive return to the pool last month, he easily won the 100m, 200m, 400m and 1,500m freestyle events at the 88th Dong-A meet, which doubles as a national trial.
His positive doping test was only revealed in January last year, and was initially blamed by Park's management team on the incompetence of a doctor at the hospital where the swimmer was receiving treatment.
Medeiros under microscope
Brazilian swimmer Etiene Medeiros faces the prospect of missing the upcoming Olympic Games after failing a doping test, authorities confirmed on Wednesday.
The 25-year-old was found to have traces of fenoterol in her urine during an out-of-competition test last month. Results of a B sample confirmed the presence of the banned substance.
Fenoterol is banned by the World Anti-Doping Agency because of its properties as a stimulant that increases hormone production.
"On June 15 the ABCD (Brazilian anti-doping authority) stated the facts to the CBDA (Brazilian swimming confederation) so that the confederation can begin disciplinary proceedings," the ABCD said in a statement.
Medeiros, who has qualified for the 50m freestyle, 100m freestyle and 100m backstroke at the Rio Olympics in August, said she unwittingly took the substance as part of her medication for asthma.
She is expected to appeal the decision in the coming days.