The Court of Arbitration for Sport upheld the World Anti-Doping Agency's appeal to clear Thys after South African authorities failed to hear his case.
The CAS panel said, in a ruling published this week, it was "undisputed" that Thys tested positive for norandrosterone after winning his third Seoul title in 2006.
But it agreed with WADA that "Mr. Thys's due process rights are seemingly being ignored" in South Africa.
The South African athletics federation had banned Thys for two years and seven months in December 2008. CAS cleared Thys in 2009 because of laboratory errors handling the athlete's urine samples in South Korea.
One year later, Switzerland's supreme court then ordered the case reheard in South Africa. Judges agreed with the athletics federation's appeal that its anti-doping rules should not have allowed CAS to process the case.
However, the case stalled again prompting WADA to intervene with the South Africa sports ministry and CAS to uphold the 40-year-old Thys's rights.
The case returned to Lausanne for a second hearing in October.
Athletics South Africa wrote to the sports court that it had "experienced a financial crisis" and could not afford to send lawyers to the session.