The 21-year-old Olympic, Commonwealth and world champion was disqualified from the 400-meter freestyle at the Australian selection trials in Sydney on Saturday after overbalancing into the water before the gun sounded to start his qualifying heat.
Thorpe returned to his position in the fourth lane but was approached by meeting referee John Keppie and informed of his disqualification for a false start.
Two subsequent appeals against the decision failed and Thorpe's disqualification was confirmed.
Thorpe, who became the sport's youngest world champion in 1998 at age 15, looked stunned as he left the poolside and lodged an immediate appeal, claiming the swimmers had been held too long on the blocks and that he had heard a noise before falling into the water.
2014: The Year in Music [PHOTOS]