An agriculture department spokesman said tests had revealed equine encephalosis virus (EEV) in tissue samples from some of the dead horses. The virus has also been found in blood samples from several ill horses.
The disease is generally not considered as serious as African Horse Sickness, but the strain present was virulent enough to cause some deaths, the spokesman said.
However, until African Horse Sickness can be ruled out as the cause of the 13 deaths, horse movements within the zone will only be allowed by permit.
Movements will only be allowed between two hours after sunrise and two hours before sunset, to avoid the periods of the day when the midge responsible for spreading AHS is most active.
The South African thoroughbred industry faces an export ban if AHS is confirmed within the Western Cape zone.
While exports are currently halted, the European Union, a crucial market for the industry, will not review South Africa's export status until final test results confirm the causes of the deaths.