Agriculture Minister Rory McEwen said the move, effective from Tuesday, reflected the national declaration that Australia was again free of the disease.
"It has been an extensive campaign, even for unaffected states like South Australia, and the declaration that Australia is free of equine influenza signals the end of the emergency response," Mr McEwen said.
"I'd like to thank all horse owners in South Australia for their cooperation and support in ensuring we remained free of horse flu during the period of restrictions.
"However, while the emergency is over, we must continue to be vigilant and use the knowledge we have gained to continue to protect the industry."
South Australia's chief veterinary officer Rob Rahaley said while all restrictions on horses had been lifted the industry had decided to maintain a voluntary register of events.
EI entered Australia through a NSW quarantine centre, then spread through NSW and Queensland, shutting down the racing industry in those states for three months.
The EI breakout led to the cancellation of the 2007 Sydney Spring Carnival and the Queensland Summer Carnival, threatened the Melbourne Cup and disrupted breeding, exports and equestrian events.
© 2008 AAP